rRNA rate difference in new version.

getzlab / rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization

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rRNA rate difference in new version. #62

Closed bishwaG closed 2 years ago

bishwaG commented 3 years ago

Hi, We have been using RNA-SeQC v1.1.8 for quite long. Recently, we have started using version 2.3.5, but we are getting rRNA rate 100 fold lower than the older version. Is rRNA rate calculated differently in RNA-SeQC2 ?

agraubert commented 3 years ago

Hey!

Yes, RNA-SeQC 1 and 2 compute rRNA rate very differently. It's been a while since I last looked at v1 code or documentation, but as I recall, v1 takes a list of rRNA intervals as an input, and intersects that with reads. In v2, we use rRNA regions defined in the GTF input file. If a read intersects with any GTF feature which contains "rRNA" in the transcript type field, the read is classified as ribosomal.

I hope that helps. Please let me know if you have any other questions