Chimeric alignment with AS = 0 ?
karlestira opened this issue · comments
STAR will give AS(local alignment score) tag = 0 when doing chimeric align. This makes it difficult to select minimum mismatch reads for next analysis steps.
Is it possible to give AS correctly in chimeric alignments?
Furthermore, is it possible to provide local alignment score for single read(not total score for two mates) using another tag like aS?
Presently this is not possible.