ATAC-seq Spike-in control
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enhancement
- Dominant language
- Nextflow
- Stars
- 229
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- Avg merge
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Description
Description of feature
I have a bulk ATAC-seq dataset that used a spike-in Drosophila DNA control. Info about the kit used can be found here. It would be great if a feature was developed to account for spike-in controls for atac-seq similar to the CUT&RUN work flow.
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 reviewing the existing CUT&RUN workflow and the ATAC-seq pipeline to understand how spike-in controls are currently handled elsewhere. Define the required inputs, normalization behavior, and validation criteria for Drosophila spike-in data; the work is done when the workflow supports this use case with documented, reproducible validation.
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
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100