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Old 07-18-2016, 08:55 AM   #1
KamilSJaron
Junior Member
 
Location: Switzerland

Join Date: Apr 2016
Posts: 7
Lightbulb bowtie2 bit 2 of the flag

Hello,

I am wondering what does mean "The second bit (2 in decimal, 0x2 in hexadecimal) is set if the read is part of a pair that aligned in a paired-end fashion."

I have mate pair reads mapped with following entries in sam:

Code:
H8:C19M1ACXX:5:1101:6777:2322   97      Sc_hox  1694486 42      101M    =       1691781 -2806   AGCCGGGCTGGAGCTTACCTGGCTGACAGGAACTTCTCTGGCTAGCATATACGATTTTCGGTGCACCGTGTAGATCTGCTTGGAGATTACTAGTAAGTGTC   CCCFFFFFHHHHHJJJJJJHGHJJJIIIIJIIJIIJJJJIIJJJIJJJJJIIJGIIIJGHHHFFFEE>;A?CCDDDDCCDDDB:CCDCCACCCCBCB?ACD   AS:i:-10        XN:i:0  XM:i:2  XO:i:0  XG:i:0  NM:i:2  MD:Z:93G0G6     YS:i:0  YT:Z:DP
H8:C19M1ACXX:5:1101:6777:2322   145     Sc_hox  1691781 42      101M    =       1694486 2806    TACTGCTGAAGGCAATATTAGTTCCCCTCACAATGCGAAACTAATGTTATAGATTATATTGAAAACTCATTGGTACTGTAAACTATATCATAAACATAGTA   CDDDDCDEEEEEEEFFFFFFHHHIIIJJJIHJJIJIIJJHJJIJJIIJIHHIJJJIJIIJJJIGHFJIIJJJJJGJJJJJJJJJJJJJHHHHHFFFFFCCC   AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:101        YS:i:-10        YT:Z:DP
Bitflags of those reads in binary formats are (from left to right 1 2 4 8 16 32 64 128)

1 0 0 0 0 1 1 0
1 0 0 0 1 0 0 1

It seems that both reads are well aligned (full length), they are bout 3k from each other, they are on other strains...

The only thing I can not understand is, why it has not bit 2 activated, because everything else looks fine to me...

Cheers
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