rule-download_ncbi_genome (explore)

rule-download_ncbi_genome

https://w3id.org/np/RAFYWQDUAdw306fSQ2FD6qIonLbWFPVTlQwH2C3bwoPrE/rule-download_ncbi_genome

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🚩 Minted in Nanopublication

Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE Dataset comment... approve/disapprove... edit as derived nanopublication...

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../config-1

config-1

http://purl.org/dc/terms/identifier

identifier

(this is a literal)

"config.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../config-1

config-1

https://schema.org/text

text

(this is a literal)

"samples: samples.csv ref: species: "Drosophila melanogaster" genome: "" annotation: "" accession: "GCF_000001215.4" ensembl_species: "" # e.g., "homo_sapiens" build: "" # e.g., "GRCh38" release: "" # e.g., "105" read_filter: min_length: 200 minimap2: index_opts: "" opts: "" maximum_secondary: 100 secondary_score_ratio: 1.0 samtools: samtobam_opts: "-b" bamsort_opts: "" bamindex_opts: "" bamstats_opts: "" quant: salmon_libtype: "U" deseq2: fit_type: "" design_factors: - "condition" lfc_null: 1.0 alt_hypothesis: "greaterAbs" point_width: 20 mincount: 10 alpha: 0.05 threshold_plot: 10 colormap: "Blues" figtype: "png" batch_effect: - "" isoform_analysis: FLAIR: true qscore: 1 exp_thresh: 10 col_opts: "--annotation_reliant generate --generate_map --stringent" protein_annotation: lambda: false uniref: "https://ftp.imp.fu-berlin.de/pub/lambda/index/lambda3/gen_0/uniref50_20230713.lba.gz" num_matches: 3"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../dataset

dataset

http://www.w3.org/1999/02/22-rdf-syntax-ns#type

type

https://schema.org/Dataset

Dataset

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../dataset

dataset

https://w3id.org/np/snakemake/describesWorkflow

describesWorkflow

(this is a literal)

"RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../dataset

dataset

https://w3id.org/np/snakemake/description

description

(this is a literal)

"This workflow performs differential expression analysis of RNA-seq data obtained from Oxford Nanopore long-read sequencing technology. First a transcriptome FASTA is constructed using gffread [https://github.com/gpertea/gffread]. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2 [https://github.com/lh3/minimap2]. Next quantification is performed using salmon [https://github.com/COMBINE-lab/salmon] before normalization and differential expression analysis are conducted by PyDESeq2 [https://github.com/owkin/PyDESeq2]. The workflow can optionally analyze splice-isoforms through integrating the FLAIR [https://github.com/BrooksLabUCSC/flair] workflow. Additionaly, NanoPlot [https://github.com/wdecoster/NanoPlot] is employed to analyze initial sequencing data and QualiMap [https://github.com/EagleGenomics-cookbooks/QualiMap] is used to evaluate mapping results."

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../dataset

dataset

https://w3id.org/np/snakemake/generatedAt

generatedAt

(this is a literal)

"2026-05-05T15:42:06.149516+00:00"

(xsd:dateTime) .

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../dataset

dataset

https://w3id.org/np/snakemake/hasConfigurationSection

hasConfigurationSection

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-configuration

workflow-configuration

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../dataset

dataset

https://w3id.org/np/snakemake/hasRuleSection

hasRuleSection

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-alignment_qa

rule-alignment_qa

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"sorted_alignments/{sample}_sorted.bam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-alignment_qa

rule-alignment_qa

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"QC/qualimap/{sample}"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-alignment_qa

rule-alignment_qa

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/qualimap/bamqc/environment.yaml@v4.4.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-alignment_qa

rule-alignment_qa

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v4.4.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-alignment_qa_report

rule-alignment_qa_report

https://w3id.org/np/snakemake/hasInput

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(this is a literal)

"QC/qualimap/{sample}"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-alignment_qa_report

rule-alignment_qa_report

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"qualimap/{sample}/qualimapReport.html"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-alignment_qa_report

rule-alignment_qa_report

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/base.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_index

rule-bam_index

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"sorted_alignments/{sample}_sorted.bam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_index

rule-bam_index

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"sorted_alignments/{sample}_sorted.bam.bai"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_index

rule-bam_index

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/samtools/index/environment.yaml@v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_index

rule-bam_index

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_sort

rule-bam_sort

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"alignments/{sample}.bam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_sort

rule-bam_sort

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"sorted_alignments/{sample}_sorted.bam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_sort

rule-bam_sort

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/samtools/sort/environment.yaml@v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_sort

rule-bam_sort

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_stats

rule-bam_stats

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"alignments/{sample}.bam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_stats

rule-bam_stats

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"QC/bamstats/{sample}.txt"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_stats

rule-bam_stats

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/samtools/stats/environment.yaml@v3.13.4"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_stats

rule-bam_stats

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v3.13.4"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_to_bed

rule-bam_to_bed

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"sorted_alignments/{sample}_sorted.bam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_to_bed

rule-bam_to_bed

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"sorted_alignments/{sample}_sorted.bam.bai"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_to_bed

rule-bam_to_bed

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/beds/{sample}.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_to_bed

rule-bam_to_bed

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/flair.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_flair_genome_index

rule-build_flair_genome_index

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/genomic.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_flair_genome_index

rule-build_flair_genome_index

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"index/flair_genome_index.mmi"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_flair_genome_index

rule-build_flair_genome_index

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_flair_genome_index

rule-build_flair_genome_index

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_minimap_index

rule-build_minimap_index

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"transcriptome/corrected_transcriptome.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_minimap_index

rule-build_minimap_index

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"index/transcriptome_index.mmi"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_minimap_index

rule-build_minimap_index

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/minimap2/index/environment.yaml@v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_minimap_index

rule-build_minimap_index

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-concatenate_beds

rule-concatenate_beds

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/beds/barcode10.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-concatenate_beds

rule-concatenate_beds

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/beds/barcode11.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-concatenate_beds

rule-concatenate_beds

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/beds/barcode12.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-concatenate_beds

rule-concatenate_beds

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/beds/barcode13.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-concatenate_beds

rule-concatenate_beds

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/beds/barcode15.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-concatenate_beds

rule-concatenate_beds

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/beds/barcode16.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-concatenate_beds

rule-concatenate_beds

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/beds/all_samples.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-concatenate_beds

rule-concatenate_beds

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/base.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-correct_transcriptome

rule-correct_transcriptome

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"transcriptome/transcriptome.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-correct_transcriptome

rule-correct_transcriptome

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"transcriptome/corrected_transcriptome.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-correct_transcriptome

rule-correct_transcriptome

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/gffread.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-count_reads

rule-count_reads

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"alignments/{sample}.bam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-count_reads

rule-count_reads

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"transcriptome/corrected_transcriptome.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-count_reads

rule-count_reads

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"counts/{sample}_salmon/quant.sf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-count_reads

rule-count_reads

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/salmon.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2

rule-deseq2

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"de_analysis/all.rds"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2

rule-deseq2

https://w3id.org/np/snakemake/hasOutput

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"de_analysis/{factor}_{prop_a}_vs_{prop_b}_MA_plot.svg"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2

rule-deseq2

https://w3id.org/np/snakemake/hasOutput

hasOutput

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"de_analysis/{factor}_{prop_a}_vs_{prop_b}_count_heatmap.svg"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2

rule-deseq2

https://w3id.org/np/snakemake/hasOutput

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"de_analysis/{factor}_{prop_a}_vs_{prop_b}_dispersion_plot.svg"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2

rule-deseq2

https://w3id.org/np/snakemake/hasOutput

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"de_analysis/{factor}_{prop_a}_vs_{prop_b}_l2fc.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2

rule-deseq2

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"de_analysis/{factor}_{prop_a}_vs_{prop_b}_sample_heatmap.svg"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2

rule-deseq2

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"de_analysis/{factor}_{prop_a}_vs_{prop_b}_top_count_heatmap.svg"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2

rule-deseq2

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/deseq2.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2_init

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https://w3id.org/np/snakemake/hasInput

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"/fshpc/meesters/projects/snakemake-workflows/rna-longseq-de-isoform/config/demo/samples.csv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2_init

rule-deseq2_init

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"merged/all_counts_gene.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2_init

rule-deseq2_init

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"de_analysis/all.rds"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2_init

rule-deseq2_init

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"de_analysis/normcounts.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2_init

rule-deseq2_init

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/deseq2.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ensembl_annotation

rule-download_ensembl_annotation

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"references/ensembl_annotation.gff3"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ensembl_annotation

rule-download_ensembl_annotation

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-annotation/environment.yaml@v7.5.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ensembl_annotation

rule-download_ensembl_annotation

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v7.5.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ensembl_genome

rule-download_ensembl_genome

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"references/ensembl_genome.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ensembl_genome

rule-download_ensembl_genome

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/reference/ensembl-sequence/environment.yaml@v7.5.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ensembl_genome

rule-download_ensembl_genome

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v7.5.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ncbi_annotation

rule-download_ncbi_annotation

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"references/ncbi_dataset_annotation.zip"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ncbi_annotation

rule-download_ncbi_annotation

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/reference.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ncbi_genome

rule-download_ncbi_genome

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"references/ncbi_dataset_genome.zip"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ncbi_genome

rule-download_ncbi_genome

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/reference.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-filter_reads

rule-filter_reads

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"<function <lambda> at 0x7fcf6a1dce00>"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-filter_reads

rule-filter_reads

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"filter/{sample}_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-filter_reads

rule-filter_reads

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/biopython.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode10_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode11_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode12_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode13_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode15_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode16_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"index/flair_genome_index.mmi"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/genomic.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/align/flair.bam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/align/flair.bam.bai"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/align/flair.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/flair.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode10_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode11_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode12_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode13_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode15_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/barcode16_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/align/flair_all_corrected.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/genomic.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/standardized_genomic.gtf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/collapse/flair.isoforms.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/collapse/flair.isoforms.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/flair.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_correct

rule-flair_correct

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/align/flair.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_correct

rule-flair_correct

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/genomic.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_correct

rule-flair_correct

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/standardized_genomic.gtf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_correct

rule-flair_correct

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/align/flair_all_corrected.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_correct

rule-flair_correct

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/flair.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_diffexp

rule-flair_diffexp

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/quantify/flair.counts.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_diffexp

rule-flair_diffexp

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/diffexp/genes_deseq2_QCplots_{condition_value1}_v_{condition_value2}.pdf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_diffexp

rule-flair_diffexp

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/diffexp/genes_deseq2_{condition_value1}_v_{condition_value2}.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_diffexp

rule-flair_diffexp

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/diffexp/isoforms_deseq2_QCplots_{condition_value1}_v_{condition_value2}.pdf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_diffexp

rule-flair_diffexp

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/diffexp/isoforms_deseq2_{condition_value1}_v_{condition_value2}.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_diffexp

rule-flair_diffexp

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/diffexp/isoforms_drimseq_{condition_value1}_v_{condition_value2}.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_diffexp

rule-flair_diffexp

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/flair.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_plot_isoforms

rule-flair_plot_isoforms

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"<function <lambda> at 0x7fcf6a1df2e0>"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_plot_isoforms

rule-flair_plot_isoforms

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/collapse/flair.isoforms.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_plot_isoforms

rule-flair_plot_isoforms

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/quantify/flair.counts.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_plot_isoforms

rule-flair_plot_isoforms

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/plots"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_plot_isoforms

rule-flair_plot_isoforms

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/flair.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_quantify

rule-flair_quantify

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/collapse/flair.isoforms.bed"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_quantify

rule-flair_quantify

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/collapse/flair.isoforms.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_quantify

rule-flair_quantify

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/reads_manifest.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_quantify

rule-flair_quantify

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/quantify/flair.counts.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_quantify

rule-flair_quantify

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/flair.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-generate_gene_query

rule-generate_gene_query

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"de_analysis/{factor}_{prop_a}_vs_{prop_b}_l2fc.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-generate_gene_query

rule-generate_gene_query

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"transcriptome/corrected_transcriptome.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-generate_gene_query

rule-generate_gene_query

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"protein_annotation/{factor}_{prop_a}_vs_{prop_b}_de_genes.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-generate_gene_query

rule-generate_gene_query

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/biopython.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-genome_to_transcriptome

rule-genome_to_transcriptome

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/genomic.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-genome_to_transcriptome

rule-genome_to_transcriptome

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/standardized_genomic.gff"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-genome_to_transcriptome

rule-genome_to_transcriptome

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"references/genomic.fa.fai"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-genome_to_transcriptome

rule-genome_to_transcriptome

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"transcriptome/transcriptome.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-genome_to_transcriptome

rule-genome_to_transcriptome

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/gffread.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_annotation

rule-get_annotation

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"<function <lambda> at 0x7fcf6a394cc0>"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_annotation

rule-get_annotation

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"references/genomic.gff"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_annotation

rule-get_annotation

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/reference.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_genome

rule-get_genome

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"<function <lambda> at 0x7fcf6a394d60>"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_genome

rule-get_genome

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"references/genomic.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_genome

rule-get_genome

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/reference.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_indexed_protein_db

rule-get_indexed_protein_db

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"protein_annotation/index/UniRef.lba.gz"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_indexed_protein_db

rule-get_indexed_protein_db

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/wget.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_protein_names

rule-get_protein_names

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"protein_annotation/blast_results_{factor}_{prop_a}_vs_{prop_b}.m8"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_protein_names

rule-get_protein_names

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"protein_annotation/proteins_{factor}_{prop_a}_vs_{prop_b}.csv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_protein_names

rule-get_protein_names

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/biopython.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-gff_to_gtf

rule-gff_to_gtf

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/standardized_genomic.gff"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-gff_to_gtf

rule-gff_to_gtf

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"references/standardized_genomic.gtf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-gff_to_gtf

rule-gff_to_gtf

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/gffread.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-iso_analysis_report

rule-iso_analysis_report

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"iso_analysis/plots"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-iso_analysis_report

rule-iso_analysis_report

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/report/isoforms"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-iso_analysis_report

rule-iso_analysis_report

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/report/usage"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-iso_analysis_report

rule-iso_analysis_report

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/base.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-lambda_gene_annotation

rule-lambda_gene_annotation

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"protein_annotation/index/UniRef.lba.gz"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-lambda_gene_annotation

rule-lambda_gene_annotation

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"protein_annotation/{factor}_{prop_a}_vs_{prop_b}_de_genes.fa"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-lambda_gene_annotation

rule-lambda_gene_annotation

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"protein_annotation/blast_results_{factor}_{prop_a}_vs_{prop_b}.m8"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-lambda_gene_annotation

rule-lambda_gene_annotation

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/lambda3.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-map_reads

rule-map_reads

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"filter/{sample}_filtered.fq"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-map_reads

rule-map_reads

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"index/transcriptome_index.mmi"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-map_reads

rule-map_reads

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"alignments/{sample}.sam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-map_reads

rule-map_reads

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/minimap2/aligner/environment.yaml@v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-map_reads

rule-map_reads

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-merge_read_counts

rule-merge_read_counts

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"counts/barcode10_salmon/quant.sf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-merge_read_counts

rule-merge_read_counts

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"counts/barcode11_salmon/quant.sf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-merge_read_counts

rule-merge_read_counts

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"counts/barcode12_salmon/quant.sf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-merge_read_counts

rule-merge_read_counts

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"counts/barcode13_salmon/quant.sf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-merge_read_counts

rule-merge_read_counts

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"counts/barcode15_salmon/quant.sf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-merge_read_counts

rule-merge_read_counts

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"counts/barcode16_salmon/quant.sf"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-merge_read_counts

rule-merge_read_counts

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"merged/all_counts.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-merge_read_counts

rule-merge_read_counts

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/pandas.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-pca

rule-pca

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"de_analysis/all.rds"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-pca

rule-pca

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"de_analysis/pca_{variable}.svg"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-pca

rule-pca

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/deseq2.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-reads_manifest

rule-reads_manifest

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"iso_analysis/reads_manifest.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-reads_manifest

rule-reads_manifest

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/pandas.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-sam_to_bam

rule-sam_to_bam

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"alignments/{sample}.sam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-sam_to_bam

rule-sam_to_bam

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"alignments/{sample}.bam"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-sam_to_bam

rule-sam_to_bam

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"github.com/snakemake/snakemake-wrappers/bio/samtools/view/environment.yaml@v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-sam_to_bam

rule-sam_to_bam

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"v7.6.0"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-sample_qa_plot

rule-sample_qa_plot

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"<function <lambda> at 0x7fcf6a397ba0>"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-sample_qa_plot

rule-sample_qa_plot

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"NanoPlot/{sample}/NanoPlot-report.html"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-sample_qa_plot

rule-sample_qa_plot

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/nanoplot.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-standardize_gff

rule-standardize_gff

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/genomic.gff"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-standardize_gff

rule-standardize_gff

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"references/standardized_genomic.gff"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-standardize_gff

rule-standardize_gff

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/agat.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-total_sample_qa_plot

rule-total_sample_qa_plot

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"/lustre/project/nhr-zdvhpc/dtest/raw/barcode10.fastq.gz"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-total_sample_qa_plot

rule-total_sample_qa_plot

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"/lustre/project/nhr-zdvhpc/dtest/raw/barcode11.fastq.gz"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-total_sample_qa_plot

rule-total_sample_qa_plot

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"/lustre/project/nhr-zdvhpc/dtest/raw/barcode12.fastq.gz"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-total_sample_qa_plot

rule-total_sample_qa_plot

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"/lustre/project/nhr-zdvhpc/dtest/raw/barcode13.fastq.gz"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-total_sample_qa_plot

rule-total_sample_qa_plot

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"/lustre/project/nhr-zdvhpc/dtest/raw/barcode15.fastq.gz"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-total_sample_qa_plot

rule-total_sample_qa_plot

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"/lustre/project/nhr-zdvhpc/dtest/raw/barcode16.fastq.gz"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-total_sample_qa_plot

rule-total_sample_qa_plot

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"NanoPlot/NanoPlot-report.html"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-total_sample_qa_plot

rule-total_sample_qa_plot

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/nanoplot.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-transcriptid_to_gene

rule-transcriptid_to_gene

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"merged/all_counts.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-transcriptid_to_gene

rule-transcriptid_to_gene

https://w3id.org/np/snakemake/hasInput

hasInput

(this is a literal)

"references/standardized_genomic.gff"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-transcriptid_to_gene

rule-transcriptid_to_gene

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"merged/all_counts_gene.tsv"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-transcriptid_to_gene

rule-transcriptid_to_gene

https://w3id.org/np/snakemake/hasOutput

hasOutput

(this is a literal)

"merged/transcriptid_to_gene_plot.svg"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-transcriptid_to_gene

rule-transcriptid_to_gene

https://w3id.org/np/snakemake/hasSoftwarePackage

hasSoftwarePackage

(this is a literal)

"../envs/pydeseq2.yml"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-configuration

workflow-configuration

http://www.w3.org/2000/01/rdf-schema#label

label

(this is a literal)

"from workflow configuration"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-configuration

workflow-configuration

https://w3id.org/np/snakemake/hasConfigurationFile

hasConfigurationFile

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../config-1

config-1

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

http://www.w3.org/2000/01/rdf-schema#label

label

(this is a literal)

"workflow rules"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-alignment_qa

rule-alignment_qa

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-alignment_qa_report

rule-alignment_qa_report

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_index

rule-bam_index

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_sort

rule-bam_sort

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_stats

rule-bam_stats

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-bam_to_bed

rule-bam_to_bed

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_flair_genome_index

rule-build_flair_genome_index

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-build_minimap_index

rule-build_minimap_index

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-concatenate_beds

rule-concatenate_beds

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-correct_transcriptome

rule-correct_transcriptome

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-count_reads

rule-count_reads

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2

rule-deseq2

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-deseq2_init

rule-deseq2_init

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ensembl_annotation

rule-download_ensembl_annotation

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ensembl_genome

rule-download_ensembl_genome

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ncbi_annotation

rule-download_ncbi_annotation

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-download_ncbi_genome

rule-download_ncbi_genome

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-filter_reads

rule-filter_reads

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_align

rule-flair_align

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_collapse

rule-flair_collapse

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_correct

rule-flair_correct

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_diffexp

rule-flair_diffexp

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_plot_isoforms

rule-flair_plot_isoforms

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-flair_quantify

rule-flair_quantify

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-generate_gene_query

rule-generate_gene_query

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-genome_to_transcriptome

rule-genome_to_transcriptome

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_annotation

rule-get_annotation

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_genome

rule-get_genome

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_indexed_protein_db

rule-get_indexed_protein_db

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-get_protein_names

rule-get_protein_names

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-gff_to_gtf

rule-gff_to_gtf

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-iso_analysis_report

rule-iso_analysis_report

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-lambda_gene_annotation

rule-lambda_gene_annotation

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-map_reads

rule-map_reads

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-merge_read_counts

rule-merge_read_counts

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-pca

rule-pca

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-reads_manifest

rule-reads_manifest

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-sam_to_bam

rule-sam_to_bam

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-sample_qa_plot

rule-sample_qa_plot

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-standardize_gff

rule-standardize_gff

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-total_sample_qa_plot

rule-total_sample_qa_plot

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../workflow-rules

workflow-rules

https://w3id.org/np/snakemake/hasWorkflowRule

hasWorkflowRule

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../rule-transcriptid_to_gene

rule-transcriptid_to_gene

This is the identifier for the assertion of this nanopublication. https://w3id.org/np/RAFYWQDUAd.../assertion The assertion above http://www.w3.org/ns/prov#generatedAtTime

generatedAtTime

(this is a literal)

"2026-05-05T17:42:10.127924+02:00"

(xsd:dateTime) .

This is the identifier for the assertion of this nanopublication. https://w3id.org/np/RAFYWQDUAd.../assertion The assertion above http://www.w3.org/ns/prov#wasAttributedTo

wasAttributedTo

https://orcid.org/0000-0003-2408-7588

Christian Meesters

This is the identifier for this whole nanopublication. https://w3id.org/np/RAFYWQDUAd... This nanopublication http://www.w3.org/2000/01/rdf-schema#label has the label (this is a literal)

"Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE"

This is the identifier for this whole nanopublication. https://w3id.org/np/RAFYWQDUAd... This nanopublication http://purl.org/nanopub/x/hasNanopubType has the type https://schema.org/Dataset

Dataset

This is the identifier for this whole nanopublication. https://w3id.org/np/RAFYWQDUAd... This nanopublication date and time when the nanopublication was created http://purl.org/dc/terms/created was created on (this is a literal)

"2026-05-05T15:42:06.149516+00:00"

(xsd:dateTime) .

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../sig

sig

http://purl.org/nanopub/x/hasSignatureTarget has as target This is the identifier for this whole nanopublication. https://w3id.org/np/RAFYWQDUAd... this nanopublication .

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../sig

sig

http://purl.org/nanopub/x/hasAlgorithm has the algorithm (this is a literal)

"RSA"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../sig

sig

http://purl.org/nanopub/x/hasPublicKey has the public key (this is a literal)

"MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB"

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../sig

sig

http://purl.org/nanopub/x/hasSignature has the signature (this is a literal)

"LHjd3Ks5p9Ax2YTuBkkm+9XWGBHCF3gcUtngTrKu3pZgGROiXyZTDlOA5EUDjBINRLhm8yb4VSywYrW5zzeZTSwWt5mfpnCELj5+dIVjMMhuMFA10gXunV/TGXvX0qgT4a6SO8DdY9902wAw2HhZuBllp85vk6v7ernt31GiacS4dLFoTEt/vkjRevQFgl0zs5KUYXfC9srhaJK4uEA93pA0bHK5BYDvyxUQ/ciHSvAYHmnUi10AWYePx7wRLIVaacJzVvSwmn7siHo7nERAzeSXbA+AmrknL1yVPJi/isgKWkpnwmXQWOBBqevkeWq8CyfE+o3+c7V2HslNvSg1ug=="

This is a local identifier minted within the nanopublication. https://w3id.org/np/RAFYWQDUAd.../sig

sig

http://purl.org/nanopub/x/signedBy is signed by https://orcid.org/0000-0003-2408-7588

Christian Meesters

This is the identifier for this whole nanopublication. https://w3id.org/np/RAFYWQDUAd...

this nanopublication

http://purl.org/dc/terms/creator

creator

https://orcid.org/0000-0003-2408-7588

Christian Meesters

This is the identifier for this whole nanopublication. https://w3id.org/np/RAFYWQDUAd...

this nanopublication

http://purl.org/nanopub/x/signedBy

signedBy

https://orcid.org/0000-0003-2408-7588

Christian Meesters

This is the identifier for this whole nanopublication. https://w3id.org/np/RAFYWQDUAd...

this nanopublication

http://www.w3.org/ns/prov#generatedAtTime

generatedAtTime

(this is a literal)

"2026-05-05T17:42:10.127924+02:00"

(xsd:dateTime) .

This is the identifier for this whole nanopublication. https://w3id.org/np/RAFYWQDUAd...

this nanopublication

http://www.w3.org/ns/prov#wasAttributedTo

wasAttributedTo

https://orcid.org/0000-0003-2408-7588

Christian Meesters

Christian Meesters, 5 May 2026, 15:42:06 UTC

Raw formats

Full nanopublication: TriG(txt), JSON-LD(txt), N-Quads(txt), XML(txt)

Assertions only: Turtle(txt), JSON-LD(txt), N-Triples(txt), RDF/XML(txt)