Output .bed file not found in the MACS2 folder
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enhancement
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Description
I recently ran my samples through the nf-core/chipseq pipeline and now want to use ChIPseeker for annotation. However, after checking the output, I couldn’t find the MACS2 folder containing the BED file. I would appreciate any assistance with this issue.
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First steps
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Research direction
The issue concerns nf-core/chipseq output and a missing MACS2 BED file; start by reproducing the pipeline run and inspecting the reported output paths. Confirm whether a BED file is expected for this workflow and make the output available for ChIPseeker, then verify the resulting files in the pipeline output.
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Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100