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MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
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STAR index generation or mapping with --sjfbGTFfile #51

Open pansapiens opened 5 years ago

pansapiens commented 5 years ago

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 commented 5 years ago

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

serine commented 3 years ago

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