Unable to generate report for multiQC using QualiMap RNA-Seq QC


I am trying to generate MultiQC report from multiple QualiMap RNA-Seq QC files. I am using ‘usegalaxy.org’.
The MultiQC runs but does not give any output (0 bytes). I think the problem is because MultiQC is expecting genome_coverage to be the first file in the QualiMap RNA-Seq QC output. However, I don’t see any such report. genome_coverage is present in the QualiMap report, but not in the raw data folder. I’m not sure why this is happening.

MultiQC v1.8
QualiMap RNA-Seq QC v2.2.2d

P.S. MultiQC works fine with STAR .log output (v2.7.1a) and FastQC (v0.72) raw data.

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Try using the tool QualiMap Counts QC instead to generate a summary. That means you’ll want to output the optional “counts” output, not just “statistics”, when running QualiMap RNA-Seq QC.

The version of MultiQC wrapped in Galaxy doesn’t interpret QualiMap RNA-Seq QC reports (raw data). It expects QualiMap BamQC (raw data) input, only, despite the top menu label stating that the input could be from either tool. The lower menu does specify BamQC but we can see how that can be confusing. The tool wrapper could probably be updated to be clearer – we’ll follow up on that for later potential changes.

Appreciate your patience for a reply!

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Thank you for the note. It works now.

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