bowtie on small region

[yimmieg]

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

[genlyai]

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.

[biznatch]

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.