STAR index generation or mapping with --sjfbGTFfile

[pansapiens]

I noticed RNAsik does not use the--sjfbGTFfile option (and associated --sjdb* options).

Given that the GTF is usually available, does it make sense to include this either at the index generation or mapping step ? I don't have a good sense as to how much it improves mapping around splice junctions, but the manual suggests it could make a big difference.

[drpowell]

Yes, it probably should. Either using that, or doing a 2-pass alignment will give better slice junction alignments

[serine]

Maybe it should be included. The easiest way would be to start by only allowing splice junction detection with Ensembl reference. will need to set these flags

• --sjdbGTFchrPrefix
• --sjdbOverhang