SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
TopHat Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/. rebrendi Bioinformatics 11 06-22-2016 09:55 AM
Need ideas about the advantages of Blast2Go byou678 Bioinformatics 5 08-27-2011 10:47 AM
Solexa: advantages/drawbacks/comparisions bioinf Illumina/Solexa 8 12-26-2010 02:41 PM
Advantages of third-generation rubenken The Pipeline 2 10-14-2010 01:48 AM
advantages and disadvantages of adapter barcoding? seqgirl123 Illumina/Solexa 1 10-07-2009 02:54 AM

Reply
 
Thread Tools
Old 10-13-2011, 03:11 AM   #1
frymor
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 149
Question bowtie advantages over tophat

Hi everybody,

I am working of RNA-Seq data and would like to map them using bowtie and/or tophat.

I know that tophat calls for bowtie first, but it is quite difficult to set certain parameters in tophat.
bowtie on itself is therefore a bit more forthcoming. Here I can set the parameters as I wish.

So my question is:

Does it make sense to run only tophat for the complete read file, or will it be better first to run bowtie with my own parameters and than only run tophat for the reads which weren't mapped in bowtie?

Do I waste my time on the second analysis, or is it the better way?

Thanks for help
Assa
frymor is offline   Reply With Quote
Old 10-13-2011, 03:49 AM   #2
ffinkernagel
Senior Member
 
Location: Marburg, Germany

Join Date: Oct 2009
Posts: 110
Default

Tophat does need the first stage genome alignment to define 'islands' of expression.
It should be possible to convince it to use your custom bowtie output though.

(You can also make yourself a local copy of tophat, and patch the parameters it passes to bowtie. Dirty, but quick).
ffinkernagel is offline   Reply With Quote
Old 10-14-2011, 02:43 AM   #3
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

Take a look at RUM http://www.cbil.upenn.edu/RUM/userguide.php

RUM uses bowtie for optimal mapping of RNASeq alignments. In fact it would probably even be better to use have a version of RUM using a gapped aligner.
zee is offline   Reply With Quote
Old 10-14-2011, 07:23 AM   #4
kopi-o
Senior Member
 
Location: Stockholm, Sweden

Join Date: Feb 2008
Posts: 319
Default

I thought RUM already uses BLAT for the gapped alignments.
kopi-o is offline   Reply With Quote
Reply

Tags
bowtie, parameters, tophat, unmapped reads

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 08:27 PM.


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