Merged biological replicates
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Description
To whom it may concern the following is a suggestion that I brought up on the slack and we thought would be worth it to add to the repo.
In the current iteration of the pipeline there does not yet exist a step which merges bam files from different biological replicates (i.e. similar to the nf-core/ATAC pipeline). When converted to a bigwig a merged bam file with increased depth would be a better representation from which to heatmap when plotting consensus peaks in downstream analyses etc.
Best
Ryan
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
No files or tests are named. Start by examining the current pipeline's BAM-to-bigWig flow and compare it with the nf-core/ATAC approach mentioned in the issue. Done means biological replicate BAM files can be merged before bigWig generation for downstream consensus-peak heatmaps.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100