Qualimap RNA seq QC Reads genomic origin: further categorize the Exonic region to CDS, 5'UTR and 3'UTR

[xiaol...@gmail.com]

Hi, Everyone,

I have an mRNA seq dataset (.bam file with GTF of hg38) analyzed in Qualimap RNA Seq QC. Qualimap can generate a very nice pie chart of Exonic, Intronic, and Intergenic fractions. I am interested in what fractions of 5'UTR and 3'UTR in the Exonic regions and  I wonder if we could further categorize Exonic region into CDS, 5'UTR and 3'UTR into a Pie chart? 

Thanks,

Xiao

[Konstantin Okonechnikov]

Hi,

nice suggestion, it would depend if the annotation file has the corresponding tags. I created the issue accordingly, will update once it's done:

https://bitbucket.org/kokonech/qualimap/issues/70/rna-seq-qc-add-5-3-utr-cds-regions-for-the 

Best regards,

   Konstantin

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[Xiao Lei]

Hi, Konstantin,

Thank you very much for your reply and your continuous support and improvement of Qualimap.

The annotation file I downloaded is hg38.ncbiRefSeq.gtf.gz from the website (link:  https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/). This annotation file contains tag names such as exon, CDS, 5UTR, 3UTR, etc.

Best,

Xiao

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