featureCounts is often slower than it should be

MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline

https://monashbioinformaticsplatform.github.io/RNAsik-pipe/

Apache License 2.0

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featureCounts is often slower than it should be #58

Closed pansapiens closed 5 months ago

pansapiens commented 2 years ago

I believe this is because it is provided with coordinate sorted BAMs (default samtools sort) when it should be ideally provided with read name sorted BAMs (samtools sort -n or sambamba sort -n)

pansapiens commented 5 months ago

Closed with bff17da3d2f523718c36c92b0e445aa5ed272d13 by filtering secondary alignments before counting.