Does nf-core/atacseq apply an offset to each ATAC-seq fragment?
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Description
Does the pipeline apply the standard +4/-5 offsets to aligned reads to account for the precise Tn5 binding site? I have not been able to find this in the documentation or in the code base.
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Research direction
Start by checking the pipeline documentation and code base for handling of aligned ATAC-seq reads and fragment offsets. Confirm whether the standard +4/-5 Tn5 offsets are applied, then document the behavior and relevant location so the answer is discoverable.
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Assessment
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100