Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
tophat 2.0.0 and index fasta file EGrassi Bioinformatics 0 06-20-2013 05:08 AM
Tophat trouble reconstituting index Xinlitik RNA Sequencing 2 11-29-2012 05:27 AM
Tophat building Bowtie index from gtf file Aholton RNA Sequencing 5 08-31-2012 12:18 PM
tophat hg19 index madsaan Bioinformatics 1 06-10-2011 09:56 PM
Tophat and Bowtie Index Siva Bioinformatics 1 03-09-2010 01:44 PM

Thread Tools
Old 04-27-2016, 12:34 AM   #1
Location: us

Join Date: Apr 2016
Posts: 14
Default TopHat- index file

Hi all!
I am usign TopHat2 and I get this error:
Beginning TopHat run (v2.0.10)
Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version:
Checking for Samtools
Samtools version:
Checking for Bowtie index files (genome)..
Error: Could not find Bowtie index files (SaccFasta.idx.*.ebwt)

I have read in some forum that the problem is that TopHat didn't find bowtie2. Are there different in the results if I use the index-file of Bowtie1 or Bowtie2?
Thank you in advance
edeka is offline   Reply With Quote
Old 04-27-2016, 04:36 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,655

Index files for bowtie v.1 and v.2 have different formats so they can't be used interchangeably.

That said I would suggest that you upgrade TopHat to the latest version (v.2.1.1). Also include the full command you are using if you continue having issues.
GenoMax is offline   Reply With Quote
Old 04-27-2016, 07:19 AM   #3
Junior Member
Location: India

Join Date: Oct 2015
Posts: 2

or use --bowtie1 if you do not wish to use bowtie2, as mentioned in
cpad0112 is offline   Reply With Quote

bowtie, index file, 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 03:39 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO