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genomic-medicine-sweden / tomte

A nextflow pipeline for analysing expression and splicing in RNA seq data from rare disease patient
MIT License
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Calculate hemoglobin percentage #187

Open Jakob37 opened 4 days ago

Jakob37 commented 4 days ago

Description of feature

We realized that we have a large variation of percentage of reads mapping to hemoglobin in our PAX samples (5-30%) which subsequently correlates to a number of QC metrics (multimapping, GC).

Thus we want to monitor the hemoglobin content to be easily follow up on this in the future, and thus have this as one of our QC values.

So far I have calculated this fraction from the STAR output (sample.ReadsPerGene.out.tab) using a simple Python script.

Would this make sense to include in Tomte? As an optional extra calculation. (Alternatively I can add it in our "post-processing pipeline").

jemten commented 4 days ago

It sounds pretty useful to me. What do you think @Lucpen?

Lucpen commented 1 day ago

I completely agree!

Jakob37 commented 1 day ago

OK, nice! Then I'll make a PR to Tomte.