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Old 10-17-2013, 12:41 PM   #1
illuminaGA
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Default Question about SAM file.Thanks.

Hello guys

I have a very basic question.

I got a sam file after mapping by BWA and I found lots of format like this:


ILLUMINA-XXXXXX:7:FC6XXXXXXXX:2:1:8471:2169 141 * 0 0 * * 0 0 TTTTTGTTCAAAAACACTCTGGAACTTAAAAGTAAAACTCTTCCACGTACATCTCTGGCTTATTGGTGTCTTTTTCTCTTTTTGAAGGCGTTTTGAAATGG IIIIIIIIIIIIIHIIIIIIIIIIIIIFIIIIIIIIIIHIGIIIGIIIIIIIDGIIIIIGIBHGIIEGFGGIIHIDDDIIIIHHB>HC<F?C>EECAFGGD


Others like this

ILLUMINA-XXXXXX:7:FCXXXXXXXX:2:1:13814:2169 163 chr24 42647385 60 101M = 42647444 160 AAACATTGTTTATCAACATTAGATGTAACATAAATCTCTAATGTACATACCTGATGGGAAAACAAGTAAAACAATTCATATTGATGTCAACCAAATGCATA GIDGGGECEGAAGGGG@GGGGGGGGDGBIIIIHDIIIHIHGGHIIEDHIIHIIIIHIIIIIIGHHIHIHHGHDIIGHHDHBEEDIIIG<D@DDDGGGGDDD XT:A:U NM:i:3 SM:i:23 AM:i:23 X0:i:1 X1:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:44G4A15C35 XA:Z:chr24,-42545737,101M,4;

Is previous one a unmapping reads?

Thanks a lot!

Last edited by illuminaGA; 10-17-2013 at 01:34 PM.
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Old 10-17-2013, 01:24 PM   #2
dpryan
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The first read isn't mapped (neither is its mate), the second is (and so is its mate). When trying to figure out a read's flag (the second column), it's convenient to have a calculator open in "programmer" mode, so you can just type a number and see visually which bits are set.
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Old 10-17-2013, 01:35 PM   #3
illuminaGA
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[QUOTE=dpryan;119110]The first read isn't mapped (neither is its mate), the second is (and so is its mate). When trying to figure out a read's flag (the second column), it's convenient to have a calculator open in "programmer" mode, so you can just type a number and see visually which bits are set.[/QUOT

Thank you so much!
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Old 10-17-2013, 11:19 PM   #4
harryzs
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Quote:
Originally Posted by illuminaGA View Post
Hello guys

I have a very basic question.

I got a sam file after mapping by BWA and I found lots of format like this:


ILLUMINA-XXXXXX:7:FC6XXXXXXXX:2:1:8471:2169 141 * 0 0 * * 0 0 TTTTTGTTCAAAAACACTCTGGAACTTAAAAGTAAAACTCTTCCACGTACATCTCTGGCTTATTGGTGTCTTTTTCTCTTTTTGAAGGCGTTTTGAAATGG IIIIIIIIIIIIIHIIIIIIIIIIIIIFIIIIIIIIIIHIGIIIGIIIIIIIDGIIIIIGIBHGIIEGFGGIIHIDDDIIIIHHB>HC<F?C>EECAFGGD


Others like this

ILLUMINA-XXXXXX:7:FCXXXXXXXX:2:1:13814:2169 163 chr24 42647385 60 101M = 42647444 160 AAACATTGTTTATCAACATTAGATGTAACATAAATCTCTAATGTACATACCTGATGGGAAAACAAGTAAAACAATTCATATTGATGTCAACCAAATGCATA GIDGGGECEGAAGGGG@GGGGGGGGDGBIIIIHDIIIHIHGGHIIEDHIIHIIIIHIIIIIIGHHIHIHHGHDIIGHHDHBEEDIIIG<D@DDDGGGGDDD XT:A:U NM:i:3 SM:i:23 AM:i:23 X0:i:1 X1:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:44G4A15C35 XA:Z:chr24,-42545737,101M,4;

Is previous one a unmapping reads?

Thanks a lot!

There is a tool from picard
http://picard.sourceforge.net/explain-flags.html

use the number at second column (e.g. for the first read: 141 )
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Old 10-18-2013, 12:15 PM   #5
illuminaGA
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Quote:
Originally Posted by harryzs View Post
There is a tool from picard
http://picard.sourceforge.net/explain-flags.html

use the number at second column (e.g. for the first read: 141 )
Thank you so much!!
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