Hi all,
I have tried for some time now to figure out if I can detect recombination or gene conversion using discordantly mapping reads and the FLAG information Bowtie2 outputs.
It seems like flags of 97, 145, 161 and 81 are discordant because the paired reads map the incorrect distance apart, 65 and 129 mean the reads mapped to different contigs, and 113 and 177 mean inversions. Is this correct?
Note: my information comes from this handy website: http://picard.sourceforge.net/explain-flags.html
tl;dr
If I look for paired reads with flags of 97, 145, 161 or 81 where both reads map to the same contig, is this a reasonable way to look for gene conversion or recombination events?
thanks everyone!
I have tried for some time now to figure out if I can detect recombination or gene conversion using discordantly mapping reads and the FLAG information Bowtie2 outputs.
It seems like flags of 97, 145, 161 and 81 are discordant because the paired reads map the incorrect distance apart, 65 and 129 mean the reads mapped to different contigs, and 113 and 177 mean inversions. Is this correct?
Note: my information comes from this handy website: http://picard.sourceforge.net/explain-flags.html
tl;dr
If I look for paired reads with flags of 97, 145, 161 or 81 where both reads map to the same contig, is this a reasonable way to look for gene conversion or recombination events?
thanks everyone!
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