This is a test version of Biostars. For the public version, visit https://www.biostars.org.
StringTie required filtered BAM

Hi, AUGUSTUS comes with a script which can filter BAM files 

filterBam –uniq –paired –pairwiseAlignment –in Aligned.out.ss.bam –out Aligned.out.ssf.bam

Does StringTie does any filtering by its own or would it be possible to improve StringTie by using the above script?

Thank you in advance

rna-seq gene annotation assembly
• 1,054 views • link
updated by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup • written by Ric Ric

1 answer

I woul not use filtered bam files:

  1. Firstly StringTie handles all types of reads and since the mapping context (unique, multi etc) are annotated there it knows about it.
  2. Secondly you would throw a lot of useful data away.
• 0 views • link
written by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup

Log in to answer this question.

More posts like this