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Old 08-29-2015, 07:12 PM   #1
Milestailsprowe
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Default Bowtie2 Issue:Backward call to driver()

Hello everyone I'm trying to use bowtie2-build and keep getting backward call to driver for mirror index issue.

I'm not sure what the issue is

I'm using

bowtie2-build -f genome.fa mouse_build

on the Mus_musculus build from Igenome
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Old 08-30-2015, 12:56 AM   #2
dpryan
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1. Can you post the exact error message?
2. You can probably find prebuilt indices on iGenomes.
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Old 08-30-2015, 05:15 AM   #3
GenoMax
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@milestailsprowe: If you downloaded the tar bundle from iGenomes it already has pre-built indexes for multiple aligners (e.g. look in directories /path_to/Sequence/Bowtie2Index or Sequence/BowtieIndex (for bowtie v.1)).
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Old 08-30-2015, 03:00 PM   #4
Milestailsprowe
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I retried bowtie2-build on a set I've gotten it to work and gor Total time for backward call to driver() for mirror index:1:31:06

All I did was

bowtie2-build (name of the index) and then (what I wanted it ot be called)

This is a whole new issue for me
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Old 08-31-2015, 03:21 AM   #5
GenoMax
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bowtie2-build is used to "create" new indexes from a plain fasta sequence file. Why are you trying to run bowtie2-build on a pre-built index that is ready for use with tophat/bowtie2?
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Old 08-31-2015, 12:02 PM   #6
Milestailsprowe
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Quote:
Originally Posted by GenoMax View Post
bowtie2-build is used to "create" new indexes from a plain fasta sequence file. Why are you trying to run bowtie2-build on a pre-built index that is ready for use with tophat/bowtie2?
I got it to work doing that with Bowtie2-Align before it would say Bowtie2 exited at value 1. I got the Mouse one to to work from Igenome but now a set I've done Bowtie2-Build on before is giving me this issue with the same commands.

Last edited by Milestailsprowe; 08-31-2015 at 12:12 PM.
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