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Old 02-01-2014, 01:55 PM   #1
mara34
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Default How to create bowtie2 index for use in Gene Pattern

Hi,

I'm trying to use Gene Pattern (tophat module) to analyze my RNA seq data. I'm having problems using my custom bowtie2 index (it does not come preloaded with a zebrafish index).

I downloaded the zebrafish genome from illumina igenome page, and zipped up all the bowtie2indices they gave (ie I zipped up genome.1.bt2 genome.2.bt2 etc into compiled.bt2.gz) and used that as my custom bowtie2 index. However, the error code I'm given is "unable to detect the name of the bowtie index". I have the gtf file and everything.

WHen I tried using the preloaded mouse bowtie index (with my zebrafish data), it works, and I'm able to get the sam and bam files.

Since I'm unsuccessful getting gene pattern to preload the zebrafish genome for me, I'm wondering what I can do to make my custom uploaded bowtie index to work with gene pattern.

Thanks in advance for any help!!
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Old 02-01-2014, 03:15 PM   #2
dpryan
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Don't gzip the index files.
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Old 02-02-2014, 03:48 PM   #3
mara34
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It didn't work..
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Old 02-02-2014, 04:39 PM   #4
GenoMax
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@Devon: It appears that the indexes need to be zipped for use with GenePattern.

@mara34: Did you follow the directions when you made the genome index zip files: http://www.broadinstitute.org/cancer...c/faq#zipHowTo

When you say "it didn't work" are you getting any error messages? First thing to check is the zip files. Do not gzip them but make ZIP archives (i.e. use zip instead of gzip).

Last edited by GenoMax; 02-02-2014 at 05:00 PM.
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Old 02-03-2014, 01:29 AM   #5
dpryan
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Quote:
Originally Posted by GenoMax View Post
@Devon: It appears that the indexes need to be zipped for use with GenePattern.
Guess I should have read up on that rather than just assuming that the compression was the issue I expect your zip rather than gzip suggestion will solve things.
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