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Old 05-03-2010, 02:32 AM   #1
Location: Barcelona, Spain

Join Date: Jun 2009
Posts: 38
Question SAM format: single vs multiple hits

According to the specification, there is SAM flag:
0x0100 0x0100 "the alignment is not primary (a read having split hits may have multiple primary alignment records)"

but using I could not find it i.e in Tophat SAM output file.

My problem is a follows: given that a query sequences were mapped without splits, how can I distinguish between these having just one hit in the genome (SH) and these with multiple hits?
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Old 07-17-2012, 11:29 AM   #2
Location: Boston

Join Date: Sep 2010
Posts: 36

I made a learning note for SAM format, which might be helpful to your question:
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