Black Ochre Data Labs
OverviewSpace: Independent Teams
SEEK ID: https://workflowhub.eu/projects/148
Public web page: Not specified
Organisms: No Organisms specified
WorkflowHub PALs: No PALs for this Team
Team created: 21st Mar 2023
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Teams: Black Ochre Data Labs
Organizations: Telethon Kids Institute
https://orcid.org/0000-0001-8197-3303
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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 ...
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
...
