strand of query and mate

[valei]

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)??

Thanks!

[drio]

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.