Workflows
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Created At
Updated At
Workflow type
Snakemake1
Submitter
Stevie Pederson1
Space
Independent Teams1
Creator
Stevie Pederson1
Topic annotations
ChIP-seq1
Operation annotations
ChIP-seq1
Maturity
Work-in-progress1
Work-in-progress
prepareChIPs
This is a simple snakemake
workflow template for preparing single-end ChIP-Seq data.
The steps implemented are:
- Download raw fastq files from SRA
- Trim and Filter raw fastq files using
AdapterRemoval
- Align to the supplied genome using
bowtie2
- Deduplicate Alignments using
Picard MarkDuplicates
- Call Macs2 Peaks using
macs2
A pdf of the rulegraph is available here
Full details for each step are given below. Any additional ...