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Old 01-16-2011, 08:53 PM   #1
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Default bowtie on small region


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.


yimmieg is offline   Reply With Quote
Old 01-17-2011, 06:25 AM   #2
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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.
genlyai is offline   Reply With Quote
Old 01-17-2011, 02:46 PM   #3
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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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