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  • Align sequences without quality data

    Hi

    I have a file with ~32,000 short DNA sequences (120 base pairs). I'd like to align this to the genome and generate a track for UCSC. Alignment programs I have used previously all require fastq files, and I do not have quality data. All I have is a text file with a sequence on each line. Is there another option in Galaxy, or another database that will work for this alignment?

    Thank you very much

    Kristin

  • #2
    I don't know what is available on Galaxy, but Bowtie will take fasta files as input.

    Comment


    • #3
      Thanks, I looked at this, the problem is I don't have it in fasta format either. I just have a list of sequences and am not sure how to get an interspersed <with an indentifier for each?

      Basically I was given a list of sequences as an output for probes for a selection RNA-seq experiment. The company gives it to you in this format and says to trust them things are designed properly but I would really like to check myself.

      Comment


      • #4
        Have a look at the bowtie manual, under the heading 'Input'



        Apparently it also takes what it calls 'raw data', one sequence per line,
        which sounds like what you have.

        Comment


        • #5
          Awesome, thank you so much for your help!

          Comment

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