SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
MAQ Scores & Quantify maq alignments? AnamikaDarwin Bioinformatics 5 09-19-2015 08:24 AM
MAQ Help dafil Bioinformatics 3 07-21-2010 10:39 AM
Tophat versus Maq sbmontgomery RNA Sequencing 1 03-18-2010 09:39 PM
About MAQ James Wei Bioinformatics 4 02-04-2010 05:12 AM
What is the difference between "maq match" and "maq map" cliff Bioinformatics 1 11-16-2009 02:13 PM

Reply
 
Thread Tools
Old 09-24-2009, 07:05 AM   #1
rpm16
Junior Member
 
Location: USA

Join Date: May 2009
Posts: 3
Default Using Maq with TopHat

Is it possible to use Maq with the latest version of TopHat? I would like to use Maq to align my reads to a reference genome. Then I would like to use TopHat to call RPKM based on the Maq alignments and a supplied GFF3 file. I think the original version of TopHat used Maq as the alignment program, but the current version used Bowtie. Does anyone know what needs to be done to use the Maq output as the alignment in TopHat?
rpm16 is offline   Reply With Quote
Reply

Tags
maq, seqman, tophat

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 09:25 PM.


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