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  • #16
    motif files created but not showing up in project menu

    In Windows, I load the genome database, genome region and coordinates and run "Annotate with ->Closest Gene". I get the output listed under the Project Explorer. Perfect so far.

    When I run, "Get sequence" , the fasta file is generated, but it does not show up in the Project Explorer. Likewise, when I run the "New Motif Discovery" with the previously generated FASTA sequence file, motifs are discovered and stored in the location that I specified, but they do not appear under the "Project Explorer".

    Would appreciate if anyone could point me to getting this correct.

    Thanks,
    TEB

    Comment


    • #17
      How to convert eland_extended.txt format to Aln format in order to use the Cisgenome program?

      Comment


      • #18
        Genome database file not listed on the website

        Hi Hji, I am new in the NGS analysis and is going to try the Cisgenome. I need to use a small viral genome which is not listed on the Cisgenome genome database on the website. Would you mind to let me know the way to convert a Genbank genome to a Cisgenome database file?Thank you.

        Comment


        • #19
          Hi all, I'm new here and am hoping someone may be able to help me out with a little Cisgenome issue I'm having. I've used Cisgenome successfully on a PC running Windows XP, but I'm now trying to run the program on my MacBook Pro using the Parallels program, which allows me to run Windows XP. I'm able to open the program through XP on my MAC and can load files as well, but when I try to run an application (right now I'm attempting Gibbs sampling) I get the quickly flashing black window that then disappears, and the program won't continue running. I have checked the file paths and file names, and there are no blank characters included anywhere. Also, the cisgenome.ini file does specify the correct Cisgenome installation path, so I'm at a loss as to what the problem is. Does anyone have experience running Cisgenome on Windows XP through MAC Parallels? Or perhaps it isn't possible to run the program this way. Thanks in advance, any assistance will be greatly appreciated.

          Comment


          • #20
            Cisgenome Browser - file doesn't exist

            Hello,

            i have a problem concerning the cisgenome browser and the visualization of already analyzed ChIP-Seq data through the Linux version of Cisgenome.
            When i want to visualize *.bar, *.genefile, *.cod, .... files, i always get a message - file doesn't exist!

            When i call peaks with the Windows version of cisgenome and then doubleclick on a peak - the browser opens and the data is showing in the browser. But adding additional datafiles is not possible.. - file doesn't exist..!?

            Are there any helpful suggestions???

            Thanks! tec

            Comment


            • #21
              Originally posted by tec View Post
              Hello,

              i have a problem concerning the cisgenome browser and the visualization of already analyzed ChIP-Seq data through the Linux version of Cisgenome.
              When i want to visualize *.bar, *.genefile, *.cod, .... files, i always get a message - file doesn't exist!

              When i call peaks with the Windows version of cisgenome and then doubleclick on a peak - the browser opens and the data is showing in the browser. But adding additional datafiles is not possible.. - file doesn't exist..!?

              Are there any helpful suggestions???

              Thanks! tec
              ok, the problem is solved
              we had to change the config file - src_filename=.. - to the right path of the file

              Comment


              • #22
                CisGenome does not run?

                Hi all,

                I can not make CisGenome to work on my system. I downloaded windows version, unzip, put it in C:\ and changed the ini file to the right location, but then when trying with some test files, nothing happened. It seems to me that the GUI does not connect with the executable files.

                Any body has it run on your computer, can you help please?

                Thanks,

                D.

                Comment


                • #23
                  to find binidng motif in chip on chip data

                  I have nimblegen Chip on chip data with two antibodies and want to find out common binding motif from the data could anyone point me how to proceded I know there are several softwares -chipmotif, cisgenom etc.
                  The file I have has chr position marked 1000 bp (I combined probles of different regions) and then log ratio of intensities. How to create intial file meaning Bed or else. Do I have to put these chr positions in data in USCS genome browser to get seq out put but then what will happend to score. Apology fro asking such a trivial question.

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                  • #24
                    Hello,

                    I am a rookie in applying cisgenome and now I have a problem in installing it in Linux. I have unzipped cisgenome v1.2 and entered the "cisgenome_project", after typing "makefile" it appears "-bash: makefile: command not found". If I change to run "make", I get the error "makefile:3: *** missing separator. Stop."

                    I don't know what to do, I have been searching through manuals and forums for weeks now. Any help would be greatly appreciated!

                    Thanks!

                    Comment


                    • #25
                      compile cisgenome

                      Hi lqscici,

                      the problem is that the file "makefile" in cisgenome_project is not a file in proper Makefile format as a standard "make" command would expect it, but it's a shell script.
                      You can try a
                      Code:
                      ./makefile
                      in the cisgenome_project folder (should work because of the "#! /bin/sh" in the first line), or you call it explicitely as a shell script:
                      Code:
                      sh makefile
                      I had some compilation problems related to 32/64 bit later on for ./cpp/tablesorter.cpp and ./cpp/tablesorter_str.cpp - I had to remove the "-m64" flag for the two targets before being able to compile. Just in case you get the same problem later on. Please be aware that I did not test if this has an effect on the results.

                      Cheers,
                      Holger

                      Comment


                      • #26
                        hello, i am using cisgenome for chip-chip data analysis.

                        Comment


                        • #27
                          hello everybody, I am using cisgenome for chip-chip data analysis. I am getting constant FDR .619523 for all ~900 potential binding regions in .cod file, using two sample analysis in TileMap, where I put sample > control.
                          can anybody tell me that why i m getting constsnt FDR for all 900 regions.

                          i willbe really highly thankful to all.

                          Comment


                          • #28
                            Originally posted by hklein View Post
                            Hi lqscici,

                            the problem is that the file "makefile" in cisgenome_project is not a file in proper Makefile format as a standard "make" command would expect it, but it's a shell script.
                            You can try a
                            Code:
                            ./makefile
                            in the cisgenome_project folder (should work because of the "#! /bin/sh" in the first line), or you call it explicitely as a shell script:
                            Code:
                            sh makefile
                            I had some compilation problems related to 32/64 bit later on for ./cpp/tablesorter.cpp and ./cpp/tablesorter_str.cpp - I had to remove the "-m64" flag for the two targets before being able to compile. Just in case you get the same problem later on. Please be aware that I did not test if this has an effect on the results.

                            Cheers,
                            Holger

                            Thanks for mentioning the CPU solution, it helped me a lot.

                            Comment


                            • #29
                              Originally posted by hklein View Post
                              I had some compilation problems related to 32/64 bit later on for ./cpp/tablesorter.cpp and ./cpp/tablesorter_str.cpp - I had to remove the "-m64" flag for the two targets before being able to compile. Just in case you get the same problem later on. Please be aware that I did not test if this has an effect on the results.

                              Cheers,
                              Holger

                              Thanks for mentioning the CPU solution, it helped me a lot.

                              Comment


                              • #30
                                cisGenome output (.bar or .cod) to .wig?

                                Originally posted by seidel View Post
                                Anyone know of a utility to convert .bar files to .wig files?

                                I'd be happy to write a program to do it - but any pointers for the .bar format would be helpful. I'm sure I'm not the only one who would be interested in seeing cisGenome output in the UCSC genome browser (which doesn't read .bar last I checked).

                                I need a similar program to convert sicGenome output (bar/cod) to wig, please let me know if you have got/developed such a tool.

                                Comment

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