SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Filter a SAM file by alignment score (AS) sjackman Bioinformatics 6 03-08-2016 11:44 AM
Bowtie XA, X0, X1 tags in SAM output aarvey Bioinformatics 0 10-21-2012 02:01 PM
CIGAR field of SAM file from Bowtie alignment qwsqe Bioinformatics 4 05-08-2012 05:28 AM
extract alignment from SAM with a GFF file NicoBxl Bioinformatics 4 08-02-2011 01:45 PM
SAM file from bowtie jay2008 Bioinformatics 0 12-09-2010 05:09 AM

Reply
 
Thread Tools
Old 03-05-2013, 10:18 PM   #1
neha
Member
 
Location: kolkata

Join Date: Oct 2011
Posts: 32
Default bowtie priduced SAm file does not have RG tags in alignment

Hello Everyone,

I have used bowtie for mapping my reads to human genome. Bowtie directly outputs the SAM file using -S option but then I realized that SAM file produced does not have the RG tags which is required by various other software Like GATK for variant analysis.

I figured out the way to add the RG tags in header section, but still it does not provide these tags in alignment section.

Does anyone has faced this problem before and any advice would be appreciated.

Thanks and Regards,
Neha
neha is offline   Reply With Quote
Old 03-06-2013, 12:19 AM   #2
dariober
Senior Member
 
Location: Cambridge, UK

Join Date: May 2010
Posts: 311
Default

Quote:
Originally Posted by neha View Post
Hello Everyone,

I have used bowtie for mapping my reads to human genome. Bowtie directly outputs the SAM file using -S option but then I realized that SAM file produced does not have the RG tags which is required by various other software Like GATK for variant analysis.
Hello- Have a look at Picard AddOrReplaceReadGroups it should do what you need.

Dario
dariober is offline   Reply With Quote
Old 03-06-2013, 05:48 AM   #3
kmcarr
Senior Member
 
Location: USA, Midwest

Join Date: May 2008
Posts: 1,167
Default

Quote:
Originally Posted by neha View Post
I have used bowtie for mapping my reads to human genome. Bowtie directly outputs the SAM file using -S option but then I realized that SAM file produced does not have the RG tags which is required by various other software Like GATK for variant analysis.
Both Bowtie and Bowtie2 can add read group information to the SAM output, but do not by default. You have to provide the information through command line options when you run Bowtie(2). The two versions of Bowtie have different options for adding read group information.

Bowtie uses the option --sam-RG option to add TAG:VALUE pairs to build the full read group definition. --sam-RG is used multiple times, once for each TAG:VALUE to be added to the read group definition; at a minimum the TAGs ID and SM (sample) must be included in the definition.

Code:
Example:
--sam-RG ID:HWI-SN957Lane7 --sam-RG SM:ZEN456A1 --sam-RG LB:ZEN456A1LI5 --sam-RG PI:400 --sam-RG PL:ILLUMINA
Bowtie2 is very similar except that it has separate options for specifying the read group ID (--rg-id) used only once on the command line and other read group TAG:VALUE pairs which may be used multiple times. If you use the --rg option you must also supply the --rg-id option.

Code:
Example:
--rg-id HWI-SN957Lane7 --rg SM:ZEN456A1 --rg LB:ZEN456A1LI5 --rg PI:400 --rg PL:ILLUMINA
Of course this won't help you for the SAM file you already have; in this case dariober's suggestion about Picard's AddOrReplaceReadGroups is the way to go.
kmcarr is offline   Reply With Quote
Old 03-12-2013, 02:47 AM   #4
neha
Member
 
Location: kolkata

Join Date: Oct 2011
Posts: 32
Default

Thanks kmcarr and Dario. I will try Picard utility and hope it will solve my problem.

Thanks,
Neha
neha is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:34 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO