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  • Compute paired-end distance distribution?

    I'm guessing one of the existing packages out there will do this, but haven't quite found it. If I have aligned paired-end / mate-pair data, what open source tool(s) will compute the mean & stddev of the distances between pairs?

    I may just write a Perl one as an exercise, but even then it will be useful to have a comparator.

  • #2
    Are you talking about when you have a reference genome, mapping the paired end reads onto it, and then tallying up the observed separations?

    Comment


    • #3
      Originally posted by krobison View Post
      I'm guessing one of the existing packages out there will do this, but haven't quite found it. If I have aligned paired-end / mate-pair data, what open source tool(s) will compute the mean & stddev of the distances between pairs?

      I may just write a Perl one as an exercise, but even then it will be useful to have a comparator.
      You can use the "dnaa/dutil/dbampairedenddist" C program in the DNAA package to compute a histogram of the paired end distribution. It takes as input a BAM file.

      Nils

      Comment


      • #4
        Thanks -- apologies if it was a bit unclear in the original posting -- I was looking for something that would take aligned reads as input and give the distribution as output.

        I'm not having much luck with the sourceforge pages -- the links to the files don't seem to be there.

        Comment


        • #5
          Originally posted by krobison View Post
          Thanks -- apologies if it was a bit unclear in the original posting -- I was looking for something that would take aligned reads as input and give the distribution as output.

          I'm not having much luck with the sourceforge pages -- the links to the files don't seem to be there.
          The input is an aligned file (in binary SAM format). You can checkout the latest code using git as there are no releases yet:
          Code:
           git clone git://dnaa.git.sourceforge.net/gitroot/dnaa/dnaa
          Nils

          Comment


          • #6
            Originally posted by krobison View Post
            I'm guessing one of the existing packages out there will do this, but haven't quite found it. If I have aligned paired-end / mate-pair data, what open source tool(s) will compute the mean & stddev of the distances between pairs?
            Using the mean and standard deviation implicity assume the variable you are measuring are normally distributed. This is not true for insert lengths from mapping to a reference genome, as genomic rearrangements and ambiguous mappings will cause tjhe distribution to have a fat right tail - disruptive outliers.

            The MODE, or maybe the median would be a better estimate for the centroid, and the mean absolute distance for the standard deviation.

            Comment


            • #7
              Novoalign maps reads to reference sequences and by default outputs a statistical distribution of the fragment lengths in the standard alignment report.

              Additionally you can output SAM format when running novoalign ("-o S" option) and use the DNAA package as suggested by nilshomer.

              Send me a private message or see www.novocraft.com wiki for more information.


              Originally posted by krobison View Post
              I'm guessing one of the existing packages out there will do this, but haven't quite found it. If I have aligned paired-end / mate-pair data, what open source tool(s) will compute the mean & stddev of the distances between pairs?

              I may just write a Perl one as an exercise, but even then it will be useful to have a comparator.

              Comment


              • #8
                DNAA pair-end (mate pair) distance distribution

                Originally posted by krobison View Post
                I'm guessing one of the existing packages out there will do this, but haven't quite found it. If I have aligned paired-end / mate-pair data, what open source tool(s) will compute the mean & stddev of the distances between pairs?

                I may just write a Perl one as an exercise, but even then it will be useful to have a comparator.
                Did you make it to run dnaa ?
                after adding the needed lib from samtool source and bfast tools i have the following error message :

                ~/NGSSOFT/dnaa/dutil$ gcc -o prdist dbampairedenddist.c
                /tmp/ccu8EfwQ.o: In function `main':
                dbampairedenddist.c: (.text+0x115): undefined reference to `PrintError'
                dbampairedenddist.c: (.text+0x18d): undefined reference to `samopen'
                dbampairedenddist.c: (.text+0x1c5): undefined reference to `PrintError'
                dbampairedenddist.c: (.text+0x34d): undefined reference to `samread'
                dbampairedenddist.c: (.text+0x3f9): undefined reference to `samclose'
                collect2: ld returned 1 exit status

                Is there any other alternative solution available ?

                Thanks in advance,

                Regards,
                Ramzi
                Last edited by ramouz87; 11-12-2009, 06:34 AM. Reason: bug
                Research Scientist - Bioinformatics
                Sidra Medical and Research Center

                Comment


                • #9
                  Hi,
                  I am trying to download the DNAA package from http://sourceforge.net/projects/dnaa/files/ But It seems as if the link doesn't work.

                  Comment


                  • #10
                    Ah, I have already found the download link git://dnaa.git.sourceforge.net/gitroot/dnaa/dnaa. But I couldn't download it via Mozilla Firefox.
                    Firefox doesn't know how to open this address, because the protocol (git) isn't associated with any program.

                    Comment


                    • #11
                      Originally posted by ramouz87 View Post
                      Did you make it to run dnaa ?
                      after adding the needed lib from samtool source and bfast tools i have the following error message :

                      ~/NGSSOFT/dnaa/dutil$ gcc -o prdist dbampairedenddist.c
                      /tmp/ccu8EfwQ.o: In function `main':
                      dbampairedenddist.c: (.text+0x115): undefined reference to `PrintError'
                      dbampairedenddist.c: (.text+0x18d): undefined reference to `samopen'
                      dbampairedenddist.c: (.text+0x1c5): undefined reference to `PrintError'
                      dbampairedenddist.c: (.text+0x34d): undefined reference to `samread'
                      dbampairedenddist.c: (.text+0x3f9): undefined reference to `samclose'
                      collect2: ld returned 1 exit status

                      Is there any other alternative solution available ?

                      Thanks in advance,

                      Regards,
                      Ramzi
                      Try
                      Code:
                      ./configure
                      make
                      make install
                      Use autotools when available instead of trying gcc!

                      Comment


                      • #12
                        Originally posted by MerFer View Post
                        Ah, I have already found the download link git://dnaa.git.sourceforge.net/gitroot/dnaa/dnaa. But I couldn't download it via Mozilla Firefox.
                        Firefox doesn't know how to open this address, because the protocol (git) isn't associated with any program.
                        You must use the "git" to retrieve the source code. Once git is installed, type:

                        Code:
                        git clone git://dnaa.git.sourceforge.net/gitroot/dnaa/dnaa

                        Comment

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