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  • Bowtie Output Information

    Does anyone know how to find out % aligned reads from a bowtie output file? Is there a command to do it? Is it there somewhere in the file? I did not save this information for my output files and would like to get it now.

    Thanks,
    Priyanka Surana

  • #2
    samtools flagstat a.bam

    Comment


    • #3
      Originally posted by fabrice View Post
      samtools flagstat a.bam
      I have the bowtie output in the default format not the sam format. Is there a way to convert the already existing bowtie default output to sam format which I could then convert to bam of course.

      Thanks

      Comment


      • #4
        Hi psurana,

        This does not answer your question directly but may help you out: Bowtie can output alignment in the sam format. So if you can not find a solution to your problem, you may redo the alignment with option -S (or --sam)

        Douglas

        Comment


        • #5
          Originally posted by DZhang View Post
          Hi psurana,

          This does not answer your question directly but may help you out: Bowtie can output alignment in the sam format. So if you can not find a solution to your problem, you may redo the alignment with option -S (or --sam)

          Douglas
          www.contigexpress.com
          Thanks, I might try that.

          Comment


          • #6
            I'm pretty sure that bowtie's default alignment will output one line for each aligned read, and no lines for each unaligned read, so you could do a wc -l on the file, and just count how many lines there are, and that's how many reads aligned.

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            • #7
              Default bowtie

              Hi I am just wondering if you run bowtie with -v 0 (meaning no mismatches are allowed in the alignment) and -a (meaning mulitple alignments are allowed) is the last column the number of times the read maps to the genome? 0 indicating that the alignment is unique?

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