Chimeric alignment with AS = 0 ?

alexdobin / STAR

RNA-seq aligner

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Chimeric alignment with AS = 0 ? #2091

Open karlestira opened 6 months ago

karlestira commented 6 months ago

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?

alexdobin commented 6 months ago

Presently this is not possible.