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  • uniquely mapped reads

    Hi,

    Is there anyway to report ONLY uniquely mapped reads in bowtie sam output?

  • #2
    Salut Carmen,

    The method will depend on the version of bowtie you are using.

    Are you using bowtie1 or bowtie2 ?

    Mathieu

    Comment


    • #3
      My previous reply is inappropriate.

      I posted a way to filter out multiple alignments from a SAM file, there : http://seqanswers.com/forums/showpos...45&postcount=6

      Hope this will solve your problem,
      Mathieu

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      • #4
        OK Mathieu,
        I will try your way

        Thanks for your replay

        Comment


        • #5
          Dear Mathieu,
          I used the grep command for the XS tag but in the sam output of bowtie-0.12.7 (the version I used) there isn't this tag

          Any other suggestion??

          Carmen

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          • #6
            Well, it seems that my initial question (version of bowtie) was in the end appropriate.

            In bowtie1, there is an option to report uniquely mapped reads only. From the bowtie1 manual :

            -m <int>

            Suppress all alignments for a particular read or pair if more than <int> reportable alignments exist for it. Reportable alignments are those that would be reported given the -n, -v, -l, -e, -k, -a, --best, and --strata options. Default: no limit. Bowtie is designed to be very fast for small -m but bowtie can become significantly slower for larger values of -m. If you would like to use Bowtie for larger values of -k, consider building an index with a denser suffix-array sample, i.e. specify a smaller -o/--offrate when invoking bowtie-build for the relevant index (see the Performance tuning section for details).
            Using -m 1 should fill your needs.

            Mathieu

            Comment


            • #7
              I have already used the option -m 1
              with this option the uniquely mapped reads are reported as number in the final report but in the final sam output file there are all the reads
              I'm interested in a file in which are reported only the uniquely mapped reads

              Carmen

              Comment


              • #8
                I would then switch to bowtie2 and use the method mentioned above.

                Mathieu

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                • #9
                  I will try two strategies
                  alignment with bowtie2
                  extraction of uniquely mapped reads from modified sam file with R

                  Carmen

                  Comment

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