Hi, how can I detect rearranged reads from SAM flags? I thought left read should have set 0x40 (first in pair) and right read 0x80 (second in pair), but I found this answer on similar question here:
"Yes, the second read is the second fastq you give to your mapping software, from the reads originating at adaptor 2. It's not like the DNA molecules and the adaptor molecules know which end of the DNA is closer to what your reference has arbitrarily designtated the beginning of the DNA sequence. So of course there can't be a correlation between read 1 and the read closer to the beginning of your reference."
What comes into my mind is that I can detect it with flag 0x10 (read being reverse complemented) and 0x20 (mate being reverse complemented). So i.e. when reads were sequenced in forward/reverse policy and I found reads where first is reversed and second isn't, it means that they were rearranged. But I am not sure about this. And how could be inversion detect then? Aren't flags about reverse complementary suitable for that?