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  • off-target reads

    Is there anyway to calculate predicted off-target reads based on a BED file? Thanks.

  • #2
    Would bedToBam (from bedtools) followed by Picard's CalculateHSMetrics work?

    Comment


    • #3
      bed2bam

      I do not seem to have a bed2bam.sh in bedtools 2.17.0. Can someone plese provide this file or a link? Thank you.

      Comment


      • #4
        Maybe try to re-download bedtools 2.17? It should come with it. What do you see in the bin folder that comes with it (it should be there)?

        Comment


        • #5
          bed2bam

          I re-downloaded 2.17 and do not see a bin folder. I have:

          data
          docs
          genomes
          scripts
          src
          test

          In the test folder there are .sh files but not for bed2bam

          In the src folder there is a bed2bam.cpp.

          The error that I get in cygwin is can not open perl script bed2bam:

          perl bedToBam -i Amplicons.bed -g hg1g_genome.txt > Amplicons.bam

          Thank you.

          Comment


          • #6
            You need to compile the bedtools package. What you have downloaded is the source code.

            Comment


            • #7
              bed2bam

              where do I download the correct package for cygwin? Thanks.

              Comment


              • #8
                Originally posted by cmccabe View Post
                where do I download the correct package for cygwin? Thanks.
                You will have to compile the package yourself. Bedtools is not supplied in binary form for cygwin.

                You may need to install "gcc-g++" compiler for cygwin along with the make utility, zlib, zlib-devel library. You also need to install python.

                Run the "setup.exe" for cygwin and then select these packages when you get to the package install screen.
                Last edited by GenoMax; 07-09-2013, 07:37 AM.

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                • #9
                  bed2bam

                  The bedtools package has been compiled for cygwin and the bin folder appears.

                  perl bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
                  Can't open perl script "bedToBam": No such file or directory

                  bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
                  -bash: bedToBam: command not found. I can not find the error. Thanks.

                  Comment


                  • #10
                    Originally posted by cmccabe View Post
                    The bedtools package has been compiled for cygwin and the bin folder appears.

                    perl bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
                    Can't open perl script "bedToBam": No such file or directory

                    bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
                    -bash: bedToBam: command not found. I can not find the error. Thanks.
                    You now have a compiled application. You do not need perl to run it (this is a C program BTW).

                    Run it like this (replace "path_to" with the actual directory path). This assumes that you are in the directory where the Amplicons.bed/hg19_genome files are.

                    Code:
                    $ /path_to/bin/bedToBam -i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
                    Last edited by GenoMax; 07-09-2013, 11:20 AM.

                    Comment


                    • #11
                      bed2bam

                      I get this error:
                      Microsoft Windows [Version 6.1.7601]
                      Copyright (c) 2009 Microsoft Corporation. All rights reserved.

                      C:\Users\cmccabe>cd "C:\Users\cmccabe\Desktop\bedtools-2.17.0" (both files are here)

                      C:\Users\cmccabe\Desktop\bedtools-2.17.0>\Desktop\bedtools-2.17.0/bin/bedToBam -
                      i Amplicons.bed -g hg19_genome.txt > Amplicons.bam
                      The system cannot find the path specified.

                      Thanks.

                      Comment


                      • #12
                        I haven't used Cygwin but it is weird to me that you have both "/" and "\" in your paths. You can try typing "pwd" to see the full path to the directory you are in.

                        Comment


                        • #13
                          bed2bam

                          Cygwin was only used as a compiler:

                          I am using cmd and getting that error.

                          Comment


                          • #14
                            Oh, right. Could you try changing the "/" to "\"? And make sure all of the files are in the bedtools-2.17.0 folder.

                            Comment


                            • #15
                              bed2bam

                              Here is the error:

                              Microsoft Windows [Version 6.1.7601]
                              Copyright (c) 2009 Microsoft Corporation. All rights reserved.

                              C:\Users\cmccabe>cd "C:\Users\cmccabe\Desktop\Ion_Torrent_ Software\bedtools-2.1
                              7.0" (files here)

                              C:\Users\cmccabe\Desktop\Ion_Torrent_ Software\bedtools-2.17.0>bedToBam -i Ampli
                              cons.bed -g hg19_genome.txt > Amplicons.bam
                              'bedToBam' is not recognized as an internal or external command,
                              operable program or batch file.

                              Thanks.

                              Comment

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