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  • align short query against 300M Illumina reads

    Hi,

    I have 8 short (~60nt) query sequences which I want to align to roughly 300M Illumina reads (100bp). Criteria are:

    - Allow a few mismatches (< 8)
    - Gaps are not allowed.
    - Alignment should span the entire query.
    - Report all matches, NOT just the best one.

    Do any programs exists that can accomplish this task? I was thinking BWA, or other next-gen read mappers, but these usually work with whole genomes as their database and reads as the query. The case I have here is somewhat different and may not work with these programs.

    Any ideas?

    Thanks in advance for the help.
    Last edited by hohllp; 11-17-2011, 01:49 PM.

  • #2
    Using Bioconductor

    You can simply do it in R.

    1. Install the Biostrings package

    source("http://bioconductor.org/biocLite.R")
    biocLite("Biostrings")

    2. Load the Biostrings package

    library(Biostrings)

    3. Use the matchPattern function. To get a detailed help page for it, type :

    ?matchPattern

    You'll see it has all of the options that you need for your example.

    matchPattern(pattern, subject, max.mismatch=0, min.mismatch=0, with.indels=FALSE, fixed=TRUE, algorithm="auto")

    Comment


    • #3
      Thanks. I'll give it a go.

      Comment


      • #4
        Blat should work for this too: http://genome.ucsc.edu/FAQ/FAQblat.html#blat3

        Comment


        • #5
          Originally posted by GenoMax View Post
          Blat should work for this too: http://genome.ucsc.edu/FAQ/FAQblat.html#blat3
          I am currently trying BLAT. Cannot build a database that large so splitting the 300M reads into subsets.

          Comment


          • #6
            FYI, BLAT worked well. I created a series of databases, each containing 7.5 million reads.

            Comment

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