Is it necessary to provide a BAI file to RSEM Calculate Expression when `--alignments` mode is used?

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

http://deweylab.biostat.wisc.edu/rsem/

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Is it necessary to provide a BAI file to RSEM Calculate Expression when `--alignments` mode is used? #180

Open etrh opened 2 years ago

etrh commented 2 years ago

I cannot find out whether RSEM uses the BAI file at all when in --alignment mode, do I need to have the BAI file in the same directory alongside the input BAM or is this not necessary at all?

etrh commented 2 years ago

Sorry to tag here too @pliu55. But any idea? Can I safely run rsem-calculate-expression without providing a BAI file?