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  • SHRiMP - how to obtain unique mapped reads?

    Hi,

    Can any SHRiMP users tell me how they obtain unique mapped reads (those mapped reads that only map to one position in the genome). I am mapping 50bp reads to the human genome. I have run rmapper-cs using the 'fast' and '50bp' settings.

    Thanks!

    Ian

  • #2
    nudge

    nudge for second viewing, thanks!

    Comment


    • #3
      Originally posted by idonaldson View Post
      nudge for second viewing, thanks!
      You will need to write your own post-alignment filtering script. You can bug the authors to get the output to SAM format, which would make things easier.

      Comment


      • #4
        SHRiMP now can output in SAM

        Originally posted by nilshomer View Post
        You will need to write your own post-alignment filtering script. You can bug the authors to get the output to SAM format, which would make things easier.
        The latest 6 Oct (V1.30) version has a shrimp2sam.pl script in the /Utils folder.

        Comment


        • #5
          Originally posted by idonaldson View Post
          Hi,
          Can any SHRiMP users tell me how they obtain unique mapped reads (those mapped reads that only map to one position in the genome). I am mapping 50bp reads to the human genome. I have run rmapper-cs using the 'fast' and '50bp' settings.
          This perl code will take 'hits.txt' on stdin and write 'unique_hits.txt' on stdout.

          Code:
          #!/usr/bin/perl -w
          my %seen;
          while (my $line = <>) {
            my @f = split m/\t/, $line;
            next unless @f == 10;
            next if $seen{ $f[0] }++;
            print $line;
          }

          Comment


          • #6
            Thanks for your input!

            Comment


            • #7
              Originally posted by nilshomer View Post
              You will need to write your own post-alignment filtering script. You can bug the authors to get the output to SAM format, which would make things easier.
              @Nils; I am amused The SAM munging Perl script in the 1.3.0 SHRiMP distribution is actually one authored by you.

              Comment


              • #8
                Originally posted by sci_guy View Post
                @Nils; I am amused The SAM munging Perl script in the 1.3.0 SHRiMP distribution is actually one authored by you.
                I wrote it to compare aligners a while ago for a paper that is being published tomorrow (yay). Needless to say, I have done a lot of aligner comparisons.

                Unfortunately the SHRiMP to SAM script does not support paired end reads...

                Comment


                • #9
                  I do rmmaper -cs and I am using sensitive 50bp...
                  my dates are mate pair, and I do it for _F3 file and for _R3file... The results are in two
                  different folders.

                  I am using Shrimp 1.3.2....

                  How I obtain the unique file for run the probcalc?


                  I would like to receive a answer by my personal email too: email: [email protected]

                  Thanks regards
                  Last edited by ulisses de padua; 06-06-2010, 03:02 PM. Reason: Shrimp version

                  Comment


                  • #10
                    I am trying to run SHRiMP2 on paired-end data. I have run the indexing step, and am using

                    ./gmapper-ls /Test_seq/test.fa -L hg18_combined.fa -V -N 8 -p opp-in >/Out_seq/shrimptestoutput

                    as my command. The index loads fine, and the reads file also loads, but then SHRiMP doesn't actually run and i get 0 mappings. Does anyone know how to fix this problem?

                    Many thanks.

                    Comment


                    • #11
                      Hi Rahul,
                      I believe the command you wish to run is,
                      ./gmapper-ls -L hg18_combined.fa -V -N 8 -p opp-in /Test_seq/test.fa >/Out_seq/shrimptestoutput
                      If you wish to have SAM output you can use,
                      ./gmapper-ls -E -L hg18_combined.fa -V -N 8 -p opp-in /Test_seq/test.fa >/Out_seq/shrimptestoutput
                      If you wish to output the unaligned reads in SAM format or into a separate file, please email me ([email protected]) and i can supply you with the unreleased version that supports this feature!

                      Misko

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