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  • BowTie 1 Inaccuracy 30 % ?

    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 want to run a query read file named "a493081_1.fastq" to find exact and inexact matches (allowing 1,2 and 3 substitutions - as specified in BowTie paper) for 150 bps read length.

    So, I issue the command

    Code:
    ./bowtie --all -v 0 hg19 a493081_1.fastq a.txt
    to find all alignments with 0 mismatch. And BowTie outputs,

    Code:
    # reads processed: 200000
    # reads with at least one reported alignment: 145692 (72.85%)
    # reads that failed to align: 54308 (27.15%)
    Reported 173932 alignments to 1 output stream(s)
    However, all reads are taken from hg19, so BowTie should give output "NO reads that failed to align". BowTie provides inaccurate matching, but near about 30 % inaccuracy is not similar as I found from various comparison. Can anybody help me, in what reasons this inaccuracy can happen or any procedure to make it more accurate.



    Additional: I should mention, my fastq file contains 150 bps single end reads.
    Last edited by Arupsss; 06-23-2012, 08:06 AM.

  • #2
    Any reason you are.not using bowtie2?

    Comment


    • #3
      Originally posted by genericforms View Post
      Any reason you are.not using bowtie2?
      I will use BWA, BoWtie 2 also to find a nice comparison ( I am just doing testing) . However, actually I want to know:

      Is it possible to reach error of 30 % for BowTie 1 ? Or I am making some mistakes ?

      Comment


      • #4
        Bowtie considers a 'N' in a read a mismatch - to quote the manual 'Ambiguous characters in the read mismatch all other characters.'

        Depending on how you sampled the reads, that might explain 0 to 100% of your non matching reads.

        Comment

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