I have short reads that end in a non-genomic sequence. Clipping the reads before mapping is possible but not ideal. The optimal thing for me is to use bowtie2 or STAR and allow soft clipping. This works, but the mapping is worse compared to mapping of pre-clipped reads.
I can't seem to find any option to allow "more" soft clipping. Is there any way i can make STAR/bowtie2 soft clip up to half the read (from 3' or 5' end)? Or do the mappers already do that? Where can i read on how soft clipping works?