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Old 01-08-2011, 06:53 AM   #1
lajoieb
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Default novoalign native output (strand+direction)

I am trying to extract the tag alignment strand & direction from a novoalign native output.
Not sure it's possible in this form, but alternatively is this something I can extract from a SAM formated output?

EX. novoalign native output:
PHP Code:
@HWUSI-EAS1533_0017_FC:4:1:1962:934#0/1 S       NGCCACCAGGGAACACAGTGGTGCCCAGAAGCTGGG    ([email protected]@@@@:::::::::::7:33:<:<:@    U       36      23      >chr3_13530     3306     F       .       .       .       34T>G
@HWUSI-EAS1533_0017_FC:4:1:2011:940#0/1 S       NACAGACCTCCCCTTTCCCACCAGCCCCAGAGGCCC    ####################################    QC
@HWUSI-EAS1533_0017_FC:4:1:2157:930#0/1 S       NGTCCCCATGTGTATTGAACTGGCACAAACTAAACT    '2/[email protected]@@@@@@@@@@@@@@:::::@@@@@@    U       6       108     >chr7_10986     10565    F       .      .       . 
I know the F and R represent alignment direction, but is that without regard to which strand the tag aligned to?
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Old 01-10-2011, 02:20 AM   #2
drio
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Dump your NA alignements in SAM and inspect the 5th bit of the second field of your alignments.
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Old 10-03-2011, 05:28 PM   #3
sparks
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The F & R give the direction of the alignment. This will correspond to strand if you have used a strand specific protocol to prepare your sample.
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