Try adding `circRNA_finder`

CCBR / CHARLIE

Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs

https://ccbr.github.io/CHARLIE/

MIT License

2 stars 1 forks source link

Try adding `circRNA_finder` #35

Closed kopardev closed 1 year ago

kopardev commented 1 year ago

circRNA_finder has 2 steps (perl scripts):

./runStar.pl: align with STAR
./postProcessStarAlignment.pl: process STAR output folder to generate circRNAs

kopardev commented 1 year ago

./runStar.pl does not work with the no_GTF STAR index

kopardev commented 1 year ago

./runStar.pl does not work when GTF is supplied at alignment

kopardev commented 1 year ago

Too many changes to STAR parameters need to implement this circRNA caller. It is also unsupported and not well-maintained. DO NOT include in pipeline.

kopardev commented 1 year ago

Reconsider as MapSplice takes too long and produces errors!!

kopardev commented 1 year ago

added and ON default in config.yaml... basically replacing MapSplice which is now OFF by default