Workflows
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Created At
Updated At
Workflow type
Snakemake2
Submitter
Stevie Pederson2
Space
Independent Teams2
Creator
Stevie Pederson2
Topic annotations
ChIP-seq1
Operation annotations
Transcription factor binding site prediction1
Maturity
Work-in-progress2
2
Workflows visible to you, out of a total of 2
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 ...
Work-in-progress
GRAVI: Gene Regulatory Analysis using Variable Inputs
This is a snakemake
workflow for:
- Performing sample QC
- Calling ChIP peaks
- Performing Differential Binding Analysis
- Comparing results across ChIP targets
The minimum required input is one ChIP target with two conditions.
Full documentation can be found here
Snakemake Implementation
The basic workflow is written snakemake
, requiring at least v7.7, and can be called using the following
...