Research Object Crate for prepareChIPs:
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name: - Coverage bigWig files for each individual sample are produced using CPM values (i.e. Signal Per Million Reads, SPMR) - For all combinations of target and treatment coverage bigWig files are also produced, along with fold-enrichment bigWig files
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Research Object Crate for prepareChIPs:
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author: Stevie Pederson
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date created: 2023-09-08 11:58:23.205668+00:00
date modified: 2024-03-05 12:23:16.330026+00:00
date published: 2023-09-08 11:58:23.205668+00:00
description: # prepareChIPs This is a simple `snakemake` workflow template for preparing **single-end** ChIP-Seq data. The steps implemented are: 1. Download raw fastq files from SRA 2. Trim and Filter raw fastq files using `AdapterRemoval` 3. Align to the supplied genome using `bowtie2` 4. Deduplicate Alignments using `Picard MarkDuplicates` 5. Call Macs2 Peaks using `macs2` A pdf of the rulegraph is available [here](workflow/rules/rulegraph.pdf) Full details for each step are given below. Any additional parameters for tools can be specified using `config/config.yml`, along with many of the requisite paths To run the workflow with default settings, simply run as follows (after editing `config/samples.tsv`) ```bash snakemake --use-conda --cores 16 ``` If running on an HPC cluster, a snakemake profile will required for submission to the queueing system and appropriate resource allocation. Please discuss this will your HPC support team. Nodes may also have restricted internet access and rules which download files may not work on many HPCs. Please see below or discuss this with your support team Whilst no snakemake wrappers are explicitly used in this workflow, the underlying scripts are utilised where possible to minimise any issues with HPC clusters with restrictions on internet access. These scripts are based on `v1.31.1` of the snakemake wrappers ### Important Note Regarding OSX Systems It should be noted that this workflow is **currently incompatible with OSX-based systems**. There are two unsolved issues 1. `fasterq-dump` has a bug which is specific to conda environments. This has been updated in v3.0.3 but this patch has not yet been made available to conda environments for OSX. Please check [here](https://anaconda.org/bioconda/sra-tools) to see if this has been updated. 2. The following error appears in some OSX-based R sessions, in a system-dependent manner: ``` Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : polygon edge not found ``` The fix for t…
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license: no-permission
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domain: software
domain: computer science
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concept: electronic journal
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field of research: geology
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field of research: oceanography
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IPTC: IT-computer sciences
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sentence: This index will also be used to produce the file `chrom.sizes` which is essential for conversion of bedGraph files to the more efficient bigWig files.
cite-as: Stevie Pederson. "Research Object Crate for prepareChIPs:." ROHub. Sep 08 ,2023. https://w3id.org/ro-id/3fdc0374-95f4-4c7d-928c-24dd80fbd26f.

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adapterremoval.yml
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peak_stats.smk
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samtools.yml
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prepareChIPs:
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date created: 2023-07-09 08:54:36+00:00
date modified: 2023-09-08 11:58:44.807004+00:00
description: # prepareChIPs This is a simple `snakemake` workflow template for preparing **single-end** ChIP-Seq data. The steps implemented are: 1. Download raw fastq files from SRA 2. Trim and Filter raw fastq files using `AdapterRemoval` 3. Align to the supplied genome using `bowtie2` 4. Deduplicate Alignments using `Picard MarkDuplicates` 5. Call Macs2 Peaks using `macs2` A pdf of the rulegraph is available [here](workflow/rules/rulegraph.pdf) Full details for each step are given below. Any additional parameters for tools can be specified using `config/config.yml`, along with many of the requisite paths To run the workflow with default settings, simply run as follows (after editing `config/samples.tsv`) ```bash snakemake --use-conda --cores 16 ``` If running on an HPC cluster, a snakemake profile will required for submission to the queueing system and appropriate resource allocation. Please discuss this will your HPC support team. Nodes may also have restricted internet access and rules which download files may not work on many HPCs. Please see below or discuss this with your support team Whilst no snakemake wrappers are explicitly used in this workflow, the underlying scripts are utilised where possible to minimise any issues with HPC clusters with restrictions on internet access. These scripts are based on `v1.31.1` of the snakemake wrappers ### Important Note Regarding OSX Systems It should be noted that this workflow is **currently incompatible with OSX-based systems**. There are two unsolved issues 1. `fasterq-dump` has a bug which is specific to conda environments. This has been updated in v3.0.3 but this patch has not yet been made available to conda environments for OSX. Please check [here](https://anaconda.org/bioconda/sra-tools) to see if this has been updated. 2. The following error appears in some OSX-based R sessions, in a system-dependent manner: ``` Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : polygon edge not found ``` The fix for t…
keywords: Bioinformatics, Genomics, Transcriptomics
license: no-permission
producer: Black Ochre Data Labs
programming language: #snakemake
sd date published: 2023-07-09 08:54:36+00:00
sd publisher: https://about.workflowhub.eu/
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https://w3id.org/ro-id/5cf3d332-4cd5-432a-8423-200792b8d509
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Stevie Pederson
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sig
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