About FLAG

[ardmore]

http://samtools.sourceforge.net/SAM1.pdf

FLAG: bitwise FLAG. Each bit is explained in the following table:
Bit Description
0x1 template having multiple segments in sequencing
0x2 each segment properly aligned according to the aligner
0x4 segment unmapped
0x8 next segment in the template unmapped
0x10 SEQ being reverse complemented
0x20 SEQ of the next segment in the template being reversed
0x40 the rst segment in the template
0x80 the last segment in the template
0x100 secondary alignment
0x200 not passing quality controls
0x400 PCR or optical duplicate

In the SAM format alignment section, the bitwise FLAG is as above table.
If the FLAG=165
OR FLAG=1133,
Then which category it falls in? Need a little explanation.
Thanks.

[ffinkernagel]

165 is A5 in hexadecimal - or in this case 0x1 | 0x4 | 0x20 | 0x80.

You can start by substracting the largest value smaller than your number - here 0x80 or 128 - that's set for sure. leaves you 37, that means 32 (0x20) is also set. Leaves you five, and it's easily seen that that`s 4 + 1. (With bit flags, bitwise or and addition are the same operations.

I'll leave 1133 as an exercise.

[ETHANol]

http://seqanswers.com/forums/showthread.php?t=15280