multiqc : sum up several _Log.final.out into one

Question

[ZheFrench]

Imagine in your RNASEQ workflow , you align each pair (R1/R2) with STAR ... and finally you concat your intermediate bam into only one for your sample. Usually, multiqc assume you have concat all your R1 and R2 fastq reads and you finally align once with STAR giving you only one _Log.final.out for your sample per dir.

Or if you align each pair (R1/R2) with STAR ... and finally concat in one bam ... your directory you will have several _Log.final.out whereas you treat only one sample. MultiQC will plot ever intermediate pair alignment for each _Log.final.out . Is this possible to tell MultiQC to sum up values from each _Log.final.out and plot only bar for the sample.

Answer 1

[Phil Ewels]

Hi @ZheFrench,

Phil here, author of MultiQC. Unfortunately, it's not currently possible to do what you're asking. The easiest way to get this result is to run a tool such as samtools stats on your merged bam files. MultiQC should pick up the results from this and give you a plot showing the alignment per sample. If you want to hide the intermediate results, you can prevent the STAR MultiQC module from running using -e star.

I hope that helps!

Phil

ps. We have looked into options for merging results within MultiQC (see this issue for discussion), but it would be a lot of work to generalise it across all modules (it would be a lot of new code), so I can't see that happening any time soon. But it is a possibility :)