StringTie required filtered BAM
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4.6 years ago
Ric ▴ 440

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 • 725 views
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Entering edit mode
4.6 years ago

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.
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