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  • what is this format?

    Hi, I have this format:

    AAAACTGGTTCCAGAAGTTGAGAC 1
    AAAACTGGTTCTGGCAGGTAG 1
    AAAACTGGTTGGGCTTAAAACTGC 5
    AAAACTGGTTGTAAACGGAGGAGC 2
    AAAACTGGTTTTAGATGGATAGAA 2
    AAAACTGGTTTTGCACTATTGGGC 1
    AAAACTGTAAAACAGGTGGTT 1


    what is this format and with what soft I can map it to ref genome?
    ------------
    SMART - bioinfo.uni-plovdiv.bg

  • #2
    My guess it that its a plain tab separated table with sequence and copy count.

    You can use Biopieces (www.biopieces.org) to convert this table into something useful - like FASTA format:

    Code:
    read_tab -i test.tab -k SEQ,COUNT | add_ident -k SEQ_NAME | merge_vals -k SEQ_NAME,COUNT | write_fasta -x
    >ID00000000_1
    AAAACTGGTTCCAGAAGTTGAGAC
    >ID00000001_1
    AAAACTGGTTCTGGCAGGTAG
    >ID00000002_5
    AAAACTGGTTGGGCTTAAAACTGC
    >ID00000003_2
    AAAACTGGTTGTAAACGGAGGAGC
    >ID00000004_2
    AAAACTGGTTTTAGATGGATAGAA
    >ID00000005_1
    AAAACTGGTTTTGCACTATTGGGC
    >ID00000006_1
    AAAACTGTAAAACAGGTGGTT
    You can also use Biopieces for mapping with bowtie, BWA, BLAST, etc ...


    Cheers,


    Martin
    Last edited by maasha; 11-15-2010, 05:52 AM.

    Comment


    • #3
      This format seems to have been processed with an adapter trimming program which results in varying sequence lengths.

      I assume
      "AAAACTGGTTGGGCTTAAAACTGC 5"

      needs to be interpreted as
      the sequence: "AAAACTGGTTGGGCTTAAAACTGC" was present exactly "5" times.

      What we have done with formats like this is transform it to FastA format like this:

      >1
      AAAACTGGTTGGGCTTAAAACTGC
      >2
      AAAACTGGTTGGGCTTAAAACTGC
      >3
      AAAACTGGTTGGGCTTAAAACTGC
      >4
      AAAACTGGTTGGGCTTAAAACTGC
      >5
      AAAACTGGTTGGGCTTAAAACTGC

      (to reflect the quantative aspect)

      and then map it to a genome using Bowtie or something similar.

      Good luck!

      edit: doh I was late!

      Comment


      • #4
        Thanks!,

        for the fasta I will managed to convert it, I was wandering if bowtie can get the small reads for the mapping in this fasta than..., because I saw all the times the input is fastq
        ------------
        SMART - bioinfo.uni-plovdiv.bg

        Comment


        • #5
          yes, just specify

          bowtie -f sequence_file.fa > output.txt

          This is taken from the Bowtie manual:

          -f The query input files (specified either as <m1> and <m2>, or as <s>) are FASTA files (usually having extension .fa, .mfa, .fna or similar). All quality values are assumed to be 40 on the Phred quality scale

          Comment


          • #6
            Originally posted by vebaev View Post
            AAAACTGGTTCCAGAAGTTGAGAC 1
            AAAACTGGTTCTGGCAGGTAG 1
            AAAACTGGTTGGGCTTAAAACTGC 5
            AAAACTGGTTGTAAACGGAGGAGC 2
            AAAACTGGTTTTAGATGGATAGAA 2
            AAAACTGGTTTTGCACTATTGGGC 1
            AAAACTGTAAAACAGGTGGTT 1
            It looks like someone has SORTED the reads, and COUNTED their frequency of occurrence.

            % grep -v '^>' reads.fasta | sort | uniq -c > vebaev.out

            Comment

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