Hi Biostars,

Is it fine to use STAR for bacterial data (no splicing)? Any comments/suggestions are highly appreciated.

Thanks
It should work but you need to specify `--alignIntronMax 1` to force STAR to avoid splice alignments.

Also during the genome index generation step you should put `--genomeSAindexNbases` to `min(14, log2(GenomeLength)/2 - 1)` if your bacterial genome of interest is relatively small. GenomeLength is in base pairs