SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat paired end alignment. adeslat SOLiD 5 08-07-2011 04:05 AM
Support for parallelization of paired-end alignments with BWA Fabien Campagne Bioinformatics 0 12-17-2010 05:40 AM
Does Cufflinks support single-end and paired end data together ? ersenkavak Bioinformatics 1 10-22-2010 08:26 AM
BEDTools: new tools / support for paired-end features. quinlana Bioinformatics 3 11-19-2009 06:30 AM
how paired end alignment works? totalnew Bioinformatics 8 04-27-2009 01:46 PM

Reply
 
Thread Tools
Old 03-02-2009, 01:22 PM   #1
found
Junior Member
 
Location: Miami

Join Date: Feb 2009
Posts: 8
Default why is paired-end alignment support so important

Is it because that if a read includes a paired-end, it is not easily to be found out by the current software? but why?
found is offline   Reply With Quote
Old 03-03-2009, 08:05 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

Quote:
Originally Posted by found View Post
Is it because that if a read includes a paired-end, it is not easily to be found out by the current software? but why?
I am not sure if your question makes much sense.

(A) Yes, of course pair end alignment support is important. One can get more the double the information from paired ends -- e.g., the reads themselves plus the distance between them. Chaison & Pavner have an interesting paper in Genome Research commenting on the importance of paired ends.

(B) While I suspect some alignment programs do not have paired end support it is hardly missing from many packages. It has been around The Roche-provided 'newbler' program does pair-end assembly. The ABI-provided 'corona' program does paired-end matching to a reference. That latter is not assembly per se but then the ABI SOLiD is not designed for de-novo assembly because of the short read lengths.

Perhaps your question more revolves around assembly of very short reads?

Or perhaps your question revolves around the mis-assembly due to repeat regions?

In any case please restate your question more coherently.
westerman 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 06:46 PM.


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