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  • BowTie 1 Commands ?

    From BowTie Paper I found that, it is able to find exact matches and also in exact matches. Now, from bowtie manual, I found how to build index for a genomic database. So, I build it using command,

    Code:
    bowtie-build hg19.fa hg19
    Now, I found it creates 6 files named: hg19.1.ebwt, hg19.2.ebwt, hg19.3.ebwt, hg19.4.ebwt, hg19.rev.1.ebwt, and hg19.rev.2.ebwt. From BowTie paper I found first four are Forward Index and last two are Mirror Index.

    Now, I want to run a query read file named "SRR493095.fastq" to find exact and inexact matches (allowing 1,2 and 3 substitutions - as specified in BowTie paper) for 150 bps read length. I go through BowTie manual, but it is not clear, how to get those.

    Can anybody help me:

    what commands I have to run in-order to find:

    1) Exact matching for 150 bps read length file.

    2) In Exact matching for 150 bps read length file (allowing 1,2 and 3 substitutions)

    I don't want to take output on .sam format file. I just want to see how many matches found. Thanks in advance.

    Additional: I should mention, my fastq file contains 150 bps single end reads.
    Last edited by Arupsss; 06-21-2012, 08:57 AM.

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