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Old 09-27-2010, 01:32 AM   #1
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Default strand of query and mate

Hi everybody,

I'm performing downstream pair-end analysis on Genome Analyzer II data. The reads was aligned against a reference genome using BWA that gives a BAM output. I'm a novice and I have to understand some basic topic in order to build my pipeline.

For example in the flag field I found 0x0010 (strand of the query) and 0x0020 (strand of the mate); what exactly mean they? I mean, the reads are both given in the forward strand or not? To extract the two sequences readed by GAII, have I to do some transformation (i.e. sense to antisense)??

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Old 09-27-2010, 05:36 AM   #2
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It means exactly that. That flag in your BAM record tells you what is the orientation that the aligner used to map the read. And since you are in a pair-end experiment, the other flag 0x20 comes into play also. It contains the same information but for the other end of the read.
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flag, strand

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