Picard RnaSeqMetrics CORRECT_STRAND_READS and INCORRECT_STRAND_READS

Follow

runxuan

• June 05, 2020 15:16

 

The question is about the general understanding of the method, rather than an execution problem.

How does Picard decide if an RNA-seq read alignment is a correct strand or incorrect strand  (obviously for stranded RNA-seq data)? what info does it use? Does it compare to the strand of an annotated transcript in the same region?

Thanks a lot!

Runxuan

0

• 

  Bhanu Gandham

  • June 06, 2020 23:01

  Hi ,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

  For context, check out our support policy.

   

  0

  Comment actions Permalink

Please sign in to leave a comment.