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Qualimap gene body coverage #1258

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jessakay opened this issue Jul 25, 2020 · 1 comment
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Qualimap gene body coverage #1258

jessakay opened this issue Jul 25, 2020 · 1 comment
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bug: module Bug in a MultiQC module

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@jessakay
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Is your feature request related to a problem? Please describe.
The gene coverage plot as produced by Qualimap's RNA-seq module is in units of "counts" but are displayed as "%". This also makes comparisons across samples with varying library sizes somewhat difficult
https://github.com/ewels/MultiQC/blob/8fcd6552d8b98220dad13561b37d004424ba02dd/multiqc/modules/qualimap/QM_RNASeq.py#L197

Describe the solution you'd like
Replicate what was done for RSeQC's gene body coverage module, having the option to show both absolute counts and scaled %
https://github.com/ewels/MultiQC/blob/8fcd6552d8b98220dad13561b37d004424ba02dd/multiqc/modules/rseqc/gene_body_coverage.py#L84-L89

Describe alternatives you've considered
It would be possible to replace Qualimap with RSeQC in our pipeline, but the latter is considerably slower and would necessitate requesting much longer walltimes when submitting jobs

Additional context

@ewels ewels added bug: core Bug in the main MultiQC code module: change bug: module Bug in a MultiQC module and removed bug: core Bug in the main MultiQC code module: change labels Dec 28, 2020
@ewels
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ewels commented Jun 30, 2021

Many thanks for reporting this @jessakay!

This has now been done by @ErikDanielsson in #1473 and will be included in the upcoming v1.11 release. If you get a chance to test it on dev (or after release) and confirm that it's now working as you expect, that would be amazing 👍🏻

Phil

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