change in BAGEL2 fold-change calculation between crisprseq v2.3.0 and v2.4.0dev
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Description
Description of the bug
Hi
I have two biological replicates of two samples and this is my contrast file
reference;treatment
Day0_1,Day0_2;Untreated_1,Untreated_2
When I perform the analysis with nf-core/crisprseq (2.4.0dev), BAGEL2 calculates fold change by using reference column Day0_1 (not Day0_2). But if I do this analysis with nf-core/crisprseq (2.3.0), the fold changes are instead calculated using the mean of Day0_1 and Day0_2 as the reference.
Many thanks,
Command used and terminal output
Relevant files
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System information
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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.
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Research direction
Start by reproducing the BAGEL2 calculation in nf-core/crisprseq 2.3.0 and 2.4.0dev with the supplied contrast file, comparing how Day0_1 and Day0_2 are used. No relevant files, command, or test are identified, so trace the pipeline's BAGEL2 input and calculation path. Done means the intended replicate handling is restored and the version difference is covered by a regression check.
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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
- 35/100