novoalign native output (strand+direction)

lajoieb · 01-08-2011, 07:53 AM

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    (445588888@@@@@:::::::::::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    '2/2355555@@@@@@@@@@@@@@@:::::@@@@@@    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?

drio · 01-10-2011, 03:20 AM

Dump your NA alignements in SAM and inspect the 5th bit of the second field of your alignments.

sparks · 10-03-2011, 06:28 PM

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.
Colin

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01-08-2011, 07:53 AM	#1
lajoieb Junior Member Location: Worcester MA Join Date: Jan 2009 Posts: 4	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 (445588888@@@@@:::::::::::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 '2/2355555@@@@@@@@@@@@@@@:::::@@@@@@ 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?

01-10-2011, 03:20 AM	#2
drio Senior Member Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008 Posts: 323	Dump your NA alignements in SAM and inspect the 5th bit of the second field of your alignments. __________________ -drd

10-03-2011, 06:28 PM	#3
sparks Senior Member Location: Kuala Lumpur, Malaysia Join Date: Mar 2008 Posts: 126	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. Colin