Star alignment - AS and MD tags

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4.0 years ago

mickey_95 ▴ 110

Hi,

I am trying to understand some details about alignment of sequencing reads and the alignment tags that are included in the output files in SAM format. I am using the STAR aligner and have the following question:

Will reads that map to multiple loci in the genome get assigned the same AS score and MD tag? In other words: Is the AS score/MD tag reported the maximum one obtained, i.e. for the best alignment of that specific read? I have browsed through some SAM files and it seems to be the case that different alignments of the same read have the same AS score and MD tag. But I wanted to double-check that I am understanding this correctly.

alignment ngs Star SAM format SAM alignment tags • 1.6k views

ADD COMMENT • link updated 5 months ago by xiaoleiusc ▴ 140 • written 4.0 years ago by mickey_95 ▴ 110

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I have the same question, what is the AS tag in the bam file after STAR alignment?

ADD REPLY • link 5 months ago by xiaoleiusc ▴ 140

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