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Old 05-03-2010, 02:32 AM   #1
darked89
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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 http://picard.sourceforge.net/explain-flags.html 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
sterding
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I made a learning note for SAM format, which might be helpful to your question:

http://onetipperday.blogspot.com/201...-sam-tags.html
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