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SciLifeLab / NGI-RNAseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
https://ngisweden.scilifelab.se/
MIT License
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STAR Index Generation #211

Closed apeltzer closed 6 years ago

apeltzer commented 6 years ago

Hi everyone,

just found one potential thing that could be interesting to investigate:

In the STAR Index generation phase, the option -sjdbOverhang 149 value is used (default is 100). Is there a specific reason for that? In my case, the genome generate step failed in some cases - whereas it ran through with the exact same command with default settings.

The ideal value is apparently MateLength -1, and the author suggests here, that for longer reads the default value of 100 should be fine (and the author even states that for most cases this will work fine, see the manual here (page 5) and the discussion here.

Maybe we should consider using the default here too?

ewels commented 6 years ago

Yes, I'm all for using the default 👍 I don't remember why we set this.