Go Back   SEQanswers > Applications Forums > RNA Sequencing

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
Bowtie2 long index(.bt21) and tophat sbdk82 Bioinformatics 5 09-04-2015 06:32 AM
Amazon Web Services: Tophat cannot find Bowtie2 even though Bowtie2 is in path Dr_Funkenstein RNA Sequencing 4 03-06-2014 04:55 AM
Tophat can't find Bowtie index files JohnGa Bioinformatics 38 05-17-2013 08:22 AM
Tophat - Could not find Bowtie 2 index files janaahan13 Illumina/Solexa 2 11-28-2012 08:44 AM

Thread Tools
Old 08-12-2014, 07:55 PM   #1
Location: Washington

Join Date: Jul 2014
Posts: 21
Post Tophat Can't Find Bowtie2 Index!?!?!

Hi everyone,

So I am familiar with using tophat for alignment and I used it successfully a few weeks ago with the following command:

tophat -p 4 –G ./Homo_sapiens.knownGene.hg19.sorted.withGenes.gtf --transcriptome-index=transcript_data/known hg19 ERR188021_1.fastq ERR188021_2.fastq &

When I previously ran this, it worked, however I ran it today with different fastq files and it gave me this error:

Error: Could not find Bowtie 2 index files (–G.*.bt2)

It seems like for some reason tophat thinks that -G is the base name for the index files instead of hg19. I have tried adding the full path for the hg19 but that gave the same error, I also tried getting rid of the --transcriptome-index part and that didn't change anything either. I need to have the -G reference transcript when running tophat but I don't know why this error is occuring. I tried to recreate the index files from bowtie2-build and put all 6 files into a folder titled Index which was located on my desktop and then in the above command, changed hg19 to /Path/Desktop/Index/hg19. This also failed as well.

This is really frustrating because the same exact command was working just a few weeks ago. I have top hat version 2.0.11 and bowtie2 version 2.2.3

I really need some help on this since I spent many hours trying to solve this problem. Any help would GREATLY be appreciated.


Last edited by thickrick99; 08-12-2014 at 07:58 PM.
thickrick99 is offline   Reply With Quote
Old 08-12-2014, 11:41 PM   #2
Senior Member
Location: Germany

Join Date: Apr 2012
Posts: 215

as far as I remember, tophat is quite sensitive to the correct order of parameters. The error, however, looks more like you forgot a space somewhere - put the full path to the gtf and and the index in a variable and refer to that, this makes it easier to see errors like that. I do have the same versions of tophat and bowtie2 installed and just tried the following (which worked fine)


tophat -o $tophatDir -p 8 -i 20 -G $gffFile $b2Index /path/to/your/fastq/files
WhatsOEver is offline   Reply With Quote

bowtie 2 indexes, rna-seq, tophat 2.0.11

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 12:17 PM.

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