Output bigwigs with macs2 p-value signal for every base-pair
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Description
I am looking for the MACS2 p-value signal for every base-pair, similar to the bigwigs available from ROADMAP or EPIMAP.
Had a discussion with @JoseEspinosa and he thinks it may be available using the --bdg option when calling MACS2 but this is not a parameter that is currently available:
https://github.com/nf-core/chipseq/blob/6924b669422215f9021144b251e83fc9929be1fe/main.nf#L1135-L1145
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading main.nf around lines 1135-1145 and inspect how MACS2 is currently called. Check how the --bdg option affects MACS2 outputs and how signal files are handled in the workflow. Done means the pipeline can produce bigWig output containing the MACS2 p-value signal for every base pair.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100