Hi,
I've done some testing with BWA against couple of small chromosomes. My test data is paired end data. I don't understand couple lines of my results. I made a small perl script to understand the flag field on the sam output.
That allows me to know what flags are on. I also added textual output on meaning of the fields (but it grows the code so left out here). Anyway I got following result rows in my test (cut the sequence and rest of columns out)
Now running 89 through my script gives out that 1st, 4th, 5th and 7th bits are on. So it's 1st read of pair, on reverse strand with mate unmapped. Second row has 181 so 1st, 3rd, 5th, 6th and 7th bits are on. Now this means 2nd of a pair, strand of mate and query unmapped.
My questien then. Does this mean that second pair didn't map anything and values given are actually first read of the pair?
I've done some testing with BWA against couple of small chromosomes. My test data is paired end data. I don't understand couple lines of my results. I made a small perl script to understand the flag field on the sam output.
Code:
#!/usr/bin/perl use warnings; use strict; my $dec = shift @ARGV; for (0 .. 11) { if ( $dec & 2**$_ ) { print $_+1," bit on (",2**$_,")\n" } } exit;
Code:
HWI-EAS418:1:1:0:1819#0 89 chr20 29366674 0 50M = 29366674 0 HWI-EAS418:1:1:0:1819#0 181 chr20 29366674 0 * = 29366674 0
My questien then. Does this mean that second pair didn't map anything and values given are actually first read of the pair?
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