StringTie required filtered BAM

Question

[Ric]

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

Answer 1

[Kristoffer Vitting-Seerup]

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.