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Old 07-15-2011, 09:18 AM   #1
biofreak
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Location: USA

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Default pre-built indexes

Dear all,
Where can I download bow-tie pre-built indexes for dog (canine) genome?
thanks
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Old 07-16-2011, 05:58 AM   #2
dariober
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If you can't find pre-built indexes make your own. Assuming you are happy with the ENSEMBL genome for dog, it should be just a matter of running:
Code:
cd path/to/my/bowtie/indexes
## Download ref genome
wget ftp://ftp.ensembl.org/pub/release-63/fasta/canis_familiaris/dna/Canis_familiaris.BROADD2.63.dna.toplevel.fa.gz
## Create indexes
bowtie-build Canis_familiaris.BROADD2.63.dna.toplevel.fa.gz Canis_familiaris.BROADD2.63.dna.toplevel.fa.gz
Hope this helps
Dario
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Old 07-26-2011, 03:52 PM   #3
JQL
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I thought they have canine pre-built index file?

http://bowtie-bio.sourceforge.net/index.shtml
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