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Deseq2 spike handling #2534
Deseq2 spike handling #2534
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Code looks great to me! I'm wondering if controlling it with the nextflow config is going to be more hassle, or if that should live in the script directive and be configured based on the input params. Instead, right now the end user has to figure out how to use it.
@emiller88 Could you expand on that a bit? It can't be automatically configured based on whether or not spikes are applied, because there are two modes:
... which is what Edit: I've added info on |
@emiller88 I'm going to go ahead and merge this with the two approvals. Happy to make adjustments in future PRs if you get time to expand on your suggestion at some point. |
This PR adds the ability to generate size factors in DESeq2 using a limited set of control genes, as is sometimes performed with technical controls such as ERCC spike-ins.
Based on https://support.bioconductor.org/p/9143354/ and the DESeq2 docs.
Note that if spikes are present, but the spike handling option is not selected, then the spikes are stripped so they do not participate in normalisation (since they could generate artefacts if left in place).
PR checklist
Closes #2440
versions.yml
file.label
PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware