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  • BowtieToBedFormat.jar from Vancouver Short Read Analysis Package

    Hello everyone,

    I've been having problems using the BowtieToBedFormat tool that comes with the Vancouver Short Read Analysis Package. I have bowtie files in the default output and when I go to process them with the conversion tool it produces the output files:

    Histogram.txt
    log file
    unpaired.tsv.gz
    _simple_paired_samechr.tsv.gz
    _simple_paired_spanchr.tsv.gz
    _forked_paired.tsv.gz
    _complex_paired.tsv.gz

    Great right? Well, when I unzip the files they contain nothing or txt files that are blank.

    Any suggestions? All I want to do is create a GFF or 3-column BED file from the bowtie output.


    Thanks in advance,
    Brandon

  • #2
    you can use awk to turn a bowtie text output file into a 3 column bed file

    Code:
    awk -v bp=36 '{print $3"\t"$4"\t"($4+bp)}' infile.map > outfile.bed
    set bp to however long your reads are, in this case 36bp
    cheers

    Comment


    • #3
      :O It works!! Haha.

      I had to learn what awk was, but after that I installed it on my Debian box and it worked perfectly.

      Is there a way for it to work for sequence length ranges? I do have a couple bowtie files where all of the sequence lengths are 17, but there are a few where the lengths range 15-26bps, is there a setting for that using awk?

      Thank you so much.

      Comment

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