SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Mate pair libraries with longer read length rakesh.ponnala Illumina/Solexa 4 01-16-2012 03:41 PM
tracking Illumina read pair information SES Bioinformatics 1 10-18-2011 07:40 AM
What is read depth -D100 means in samtools? ketan_bnf Bioinformatics 1 07-28-2011 07:54 PM
Tophat :: CIGAR for second read in pair polarise Bioinformatics 0 02-16-2011 04:33 AM
mate pair + single read data boetsie General 1 04-14-2010 10:08 AM

Reply
 
Thread Tools
Old 08-22-2011, 05:57 PM   #1
yhong
Junior Member
 
Location: South Korea

Join Date: Aug 2011
Posts: 3
Default first read in a pair means F3 or R3?

I am trying to extract unmapped reads afte resequencing SOLiD mate-pair reads.
This is what I know so far..

The command "samtools view -f 0x0048", gives me a list of reads whose pairs are unmapped and the reads are the first read in a pair.

The command "samtools view -f 0x0088", gives me a list of reads whose pairs are unmapped and the reads are the second read in a pair.

I have an idea that I can get a list of unmapped reads using these commands somhow.
What I don't understand is what exactly the "first" or "second" read in a pair means.
Does the "first" read in a pair represents F3 or R3?

It would be really helpful if someone can clarify this.

Thank you very much!

Best,
yhong
yhong is offline   Reply With Quote
Old 08-24-2011, 10:10 AM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

First or second is annotated by the aligner, so can you tell us which one you used?
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 02:16 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO