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:
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
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
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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