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  • #16
    Thx Prakhar,

    Sorry for my delayed response. The problem of viewing has been solved. Yeah, you are right, use ssh -X and it works! thx~

    I'm actually now trying larger-scale data on cluster, and would definitely ask for your kind help if come across new problems.

    best regard

    Comment


    • #17
      Is there anyone know the format of cnv result? For example:
      deletion chr10:6070441-6074520 4080 0.674906 0.00834134 72162.3
      It is very easy to understand the first three column mean, but is there any can explain the rest of column mean?

      Comment


      • #18
        Dear zhk,

        I had asked the same question to the author (Alex Abyzov), here is the reply.

        The output is as follows:
        CNV_type, coordinates, size, normalized_RD, p-val1, p-val2.
        p-val1 -- is from t-test
        p-val2 -- is from probability of RD valued within the region to be in
        the tails of gaussian distribution (kind a z-score).
        Regards,
        pg

        Comment


        • #19
          Thx gprakhar,

          Is that mean the larger of p-val1 and p-val2, the more confidence of the result?

          Do you find that the value of p-val2 will be very large or small sometimes? How to explain this situation?

          example:
          deletion chr10:6070441-6074520 4080 0.674906 0.00834134 72162.3

          Originally posted by gprakhar View Post
          Dear zhk,

          I had asked the same question to the author (Alex Abyzov), here is the reply.



          Regards,
          pg

          Comment


          • #20
            Hello,

            I am not sure, have used the tool on simulated data only.
            You can ask the author and please do let me know what he says.

            Regards,
            pg

            Comment


            • #21
              Hello pg,
              This is the replay from the author.

              Those p-values are not very discriminate. The major cause of false
              positives is read mismapping and sequencing biases.
              Large events are generally more trustful

              Comment


              • #22
                Hi milesgr,
                I'm in the cluster and can not get into the root. How can I install the CNVnator?

                Thanks!

                Originally posted by milesgr View Post
                Never mind, I figured it out. If anyone needs help, please feel free to post here.

                Comment


                • #23
                  Originally posted by elisadouzi View Post
                  Hi milesgr,
                  I'm in the cluster and can not get into the root. How can I install the CNVnator?

                  Thanks!
                  What do you mean by "cannot get into root". Have you downloaded ROOT package?
                  You'd better download the newest version of ROOT.(Old version may have bugs)
                  Then install CNVnator.

                  btw, ROOT is large package, you may take some patience.

                  Comment


                  • #24
                    Thanks! I got it.

                    Originally posted by CNVboy View Post
                    What do you mean by "cannot get into root". Have you downloaded ROOT package?
                    You'd better download the newest version of ROOT.(Old version may have bugs)
                    Then install CNVnator.

                    btw, ROOT is large package, you may take some patience.

                    Comment


                    • #25
                      Regards,
                      --
                      pg

                      Comment


                      • #26
                        Problems making CNVnator

                        Hi all,

                        I've got root installed, but now I'm having problems compiling CNVnator. When I type make, I get this error:

                        g++ -pthread -m64 -I/usr/local/root/bin/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
                        cc1plus: error: /usr/local/root/bin/root/include: Not a directory
                        make: *** [obj/cnvnator.o] Error 1

                        Any help much apreciated.
                        Dan

                        Comment


                        • #27
                          Try simply by typing this:

                          Code:
                          export ROOTSYS=[path to root installed directory]
                          replacing everything inside and including the square brackets by whatever directory you installed root to - e.g. /home/djaffares/root
                          then type 'make' and hit enter and it should work! Good luck Dan!
                          Last edited by dmacmillan; 01-06-2012, 02:45 PM.

                          Comment


                          • #28
                            CNVnator, still not compiling

                            Thanks for this, but still no luck. here is what I did:
                            which root
                            /usr/local/bin/root

                            export ROOTSYS=/usr/local/bin/root
                            cd software/CNVnator/src/
                            make

                            #And I still get this error.

                            g++ -pthread -m64 -I/usr/local/bin/root/include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o
                            cc1plus: error: /usr/local/bin/root/include: Not a directory
                            make: *** [obj/cnvnator.o] Error 1

                            #thanks in advance for any ideas :-)

                            Comment


                            • #29
                              You have to "cd" into CNVnator/src/samtools and then "make", so libbam.a is created.

                              Also remember to type

                              Code:
                              export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ROOTSYS}/lib
                              Then type
                              Code:
                              cd ..
                              to get back into your CNVnator/src directory and type
                              Code:
                              make
                              again

                              Comment


                              • #30
                                Also does anyone know what bin_size refers to? There is a bin size as in the .BAM bin size, but there is also the genomic bin size...

                                Comment

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