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
bowtie index problem (bowtie-build and then bowtie-inspect) tgenahmet Bioinformatics 4 09-10-2013 11:51 AM
maximum number of the reference input files for bowtie-build joseph Bioinformatics 2 09-04-2010 02:09 PM
bowtie, no .rev files produced chrisbala Bioinformatics 6 01-09-2010 06:46 AM
Bowtie-build index file generation, no *.3.ebwt, *.4.ebwt Bardj Bioinformatics 4 12-18-2009 09:32 AM

Reply
 
Thread Tools
Old 10-11-2011, 11:32 AM   #1
plasticdeath
Junior Member
 
Location: Starkville, MS

Join Date: Oct 2011
Posts: 2
Default bowtie build does not create .rev index files

when attempting to build an index using bowtie-build on a fasta genome file that is 2.1 MB, it does not create the .rev files, it produces 1.ebwt 2.ewbt 3.ebwt 4.ebwt but not the rev files. This is my first time using bowtie, all the parameters are the default options. Thanks
plasticdeath is offline   Reply With Quote
Old 10-11-2011, 12:04 PM   #2
plasticdeath
Junior Member
 
Location: Starkville, MS

Join Date: Oct 2011
Posts: 2
Default

if there is any other information you need to help me with this issue, please let me know. I have a 64 bity system with 2GB of ram and 65 GB of hard drive space free. I am using the latest 64 bit version of Ubuntu linux.
plasticdeath is offline   Reply With Quote
Old 10-01-2014, 11:24 AM   #3
JeffDu
Junior Member
 
Location: durham

Join Date: Oct 2014
Posts: 1
Default

Hi plasticdeath,
Sorry, the reply is 3 years late.

I think you might be running bowtie-build with some *.fastq files, which would only generate 4 ebwt files;
Try *.fasta then you will get all 6 index.ebwt files you want.

Typically, we should run de-novo assembly softwares first to get the assemblied fasta file. Like Velvet, SOAPdenovo etc.
After de novo assembly, we could run Bowtie to generate index files, then run bowtie to do the alignment.

hope this reply would be ok.
JeffDu is offline   Reply With Quote
Reply

Tags
.rev, bowtie, bowtie-build

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 08:19 PM.


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