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Old 01-16-2011, 08:53 PM   #1
yimmieg
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Location: Cambridge, MA

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Default bowtie on small region

hi,

i'm new to ngs and i was wondering if it's possible to build an index for a small region of a chromosome and align using bowtie.

thanks

~jimmie
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Old 01-17-2011, 06:25 AM   #2
genlyai
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Should be. All you need is a fasta file for the chromosomal region you're interested in. You can obtain this using SCGB or Galaxy. Then you can build the index per the bowtie manual.
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Old 01-17-2011, 02:46 PM   #3
biznatch
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Definitely possible, I've done it many times. I would usually go to the region I'm interested in, in UCSC Genome Browser then output the sequence from there by clicking DNA at the top then saving the page as a .txt file. It will be in the correct format for building an index with Bowtie.
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