STAR/ Bowtie2: number of matched base

Question

[ResearchR]

Dear all,

I am working on an miRNA pipeline and would like to compare bowtie2 and STAR. STAR has an option, which specifics the minimum number of matches bases to report the aligned read (--outFilterMatchNmin). I try to define the same in bowtie2, but apart from the score functions, I could not find a similar option or combination of options. Any suggestions?

Thanks and best wishes

Answer 1

[Devon Ryan]

The simplest thing to change in bowtie2 is --score-min. STAR is vastly more configurable than most any other aligner, so don't expect to be able to tweak other tools as much.