producing strandedness metrics from rnaseq data

Answered

Follow

AMN

• July 02, 2021 16:45

I have what i believe to be unstranded RNA data, and when I ran CollectRnaseqMetrics with

STRAND=NONE

I got absolutely no strandedness metrics, which I would need to confirm that my sample is indeed unstranded. is there any way to force reporting of certain metrics, such as `NUM_R1_TRANSCRIPT_STRAND_READS` and `NUM_R2_TRANSCRIPT_STRAND_READS` even when unstranded? I could obviously use the `FIRST_READ_TRANSCRIPTION_STRAND`, but i want to avoid incorrectly reporting `CORRECT_STRAND_READS`, etc. 

0

• 

  Pamela Bretscher

  • July 09, 2021 13:07

  Hi AMN,

  I don't believe there is a way to get strandedness metrics if you use STRAND=NONE as you are specifying to CollectRnaseqMetrics that there is no strandedness. You could try to use 'FIRST_READ_TRANSCRIPTION_STRAND' to get the metrics you are looking for but I don't know how accurate or useful this would be for unstranded data. 

  Best,

  Pamela

  0

  Comment actions Permalink

Please sign in to leave a comment.