SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
sam to bam conversion error, no @SQ lines in the header, missing header? efoss Bioinformatics 17 12-03-2015 04:28 AM
the header of SAM and BAM missing dongshenglulv Bioinformatics 5 10-23-2011 11:44 PM
.SAM to .BAM with SAM file header @PG emilyjia2000 Bioinformatics 13 06-14-2011 12:21 PM
how to convert sam to bam with EOF marker in header jianfeng.mao Bioinformatics 2 12-17-2010 05:56 AM
BWA: specifying SAM/BAM file header fields before read alignment? nora Bioinformatics 3 12-04-2010 09:11 PM

Reply
 
Thread Tools
Old 08-21-2009, 09:08 AM   #1
keebs42
Member
 
Location: Raleigh, NC

Join Date: May 2009
Posts: 17
Default sam/bam header lines

Could someone point me to a description of the @SQ and @RG header lines? As in:
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:1 LN:247249719
@SQ SN:2 LN:242951149
@SQ SN:3 LN:199501827
@SQ SN:4 LN:191273063
...
@RG ID:SRR001176 PL:ILLUMINA PU:BI.080220_SL-XAM_0002_FC20B2TAAXX.7 LB:Solexa-3628 PI:SM:NA12891 CN:BI
@RG ID:SRR001180 PL:ILLUMINA PU:BI.080222_SL-XAT_0001_FC13355AAXX.7 LB:Solexa-3628 PI:610 SM:NA12891 CN:BI

Most are straight forward, but I'm wondering specifically about @SQ SN: LN: and @RG PU:

Thanks!
keebs42 is offline   Reply With Quote
Old 08-21-2009, 11:25 AM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by keebs42 View Post
Could someone point me to a description of the @SQ and @RG header lines? As in:
@HD VN:1.0 GO:none SO:coordinate
@SQ SN:1 LN:247249719
@SQ SN:2 LN:242951149
@SQ SN:3 LN:199501827
@SQ SN:4 LN:191273063
...
@RG ID:SRR001176 PL:ILLUMINA PU:BI.080220_SL-XAM_0002_FC20B2TAAXX.7 LB:Solexa-3628 PI:SM:NA12891 CN:BI
@RG ID:SRR001180 PL:ILLUMINA PU:BI.080222_SL-XAT_0001_FC13355AAXX.7 LB:Solexa-3628 PI:610 SM:NA12891 CN:BI

Most are straight forward, but I'm wondering specifically about @SQ SN: LN: and @RG PU:

Thanks!
See the SAM format on the SAMtools website.
nilshomer 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 02:20 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO