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  • #46
    missing files

    Hello,

    I am having trouble with CisGenome. Whenever I try to do anything that involves generating a file the file never appears. I have changed the .ini file. CisGenome is in a path that has no spaces. There are programs in the bin folder. But whenever I do something like a file conversion, or gene annotaion, the cmd box flashes on the screen then disappears and no files appear. Any suggestions?

    gntc

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    • #47
      Too many peaks generated using Cisgenome V2 (seqpeak)

      Hi friends
      I have a strange query. I ran cisgenome for single Lane alone and in replicates as well with Input DNA as control. The problem which i'm is regarding the number of peaks. When i use the Cisgenome V2 (new and recommneded, thats what software says) with default parameters, i got around 2,10,000 peaks (for one lane) and 1,90,000 (for 2 replicates). If i increase the "Win Stat Cutoff C >=" from 3 to 4 then the peak count decreses to 70,000 and if i keep the same option to 5, then peak count comes to 67. Shall i use the new version or not. Its fast but the output which is coming is impractical. Please clear the doubts Mr Hji

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      • #48
        Originally posted by gntc View Post
        Hello,

        I am having trouble with CisGenome. Whenever I try to do anything that involves generating a file the file never appears. I have changed the .ini file. CisGenome is in a path that has no spaces. There are programs in the bin folder. But whenever I do something like a file conversion, or gene annotaion, the cmd box flashes on the screen then disappears and no files appear. Any suggestions?

        gntc
        Hi,
        I am having the exact same issue. Everything is according to the tutorial (no spaces etc.). The program launches fine and I have downloaded the rat genome. My Chip-seq data is in the Fastq format and I have converted it to aln (or atleast I think the conversion has happened since I see a file with that extension and it is a big file, thoughsmaller than the Fastq file). When I run it spits out a blank window and the command box just flashes and disappears. Any help would be greatly appreciated.
        Thanx.
        hk

        Comment


        • #49
          Originally posted by harishrk View Post
          Hi,
          I am having the exact same issue. Everything is according to the tutorial (no spaces etc.). The program launches fine and I have downloaded the rat genome. My Chip-seq data is in the Fastq format and I have converted it to aln (or atleast I think the conversion has happened since I see a file with that extension and it is a big file, thoughsmaller than the Fastq file). When I run it spits out a blank window and the command box just flashes and disappears. Any help would be greatly appreciated.
          Thanx.
          hk
          Harishrk,

          What are you trying to do exactly?

          First, when the command box flashes and disappears it means there was an error. Cisgenome doesn't say what the error was, it just terminates the program. It could be that you didn't set a proper output destination and title, the input was in an incorrect format, or that the commands (or input and output) are in a path that has spaces in it. For some reason Cisgenome doesn't work if the Desktop is in the path, so make sure to put it somewhere else.

          Secondly, aln files show genomic regions that sequences have mapped to after alignment with a program like bowtie. You should not be able to convert a fastq file to aln. Fastq files only contain the sequences and the quality of the read, no information about alignment. If you converted fastq to aln I would guess that this is your problem. You must first map your sequences to the genome, then you can convert that output to aln.

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          • #50
            Originally posted by gntc View Post
            Harishrk,

            What are you trying to do exactly?

            First, when the command box flashes and disappears it means there was an error. Cisgenome doesn't say what the error was, it just terminates the program. It could be that you didn't set a proper output destination and title, the input was in an incorrect format, or that the commands (or input and output) are in a path that has spaces in it. For some reason Cisgenome doesn't work if the Desktop is in the path, so make sure to put it somewhere else.

            Secondly, aln files show genomic regions that sequences have mapped to after alignment with a program like bowtie. You should not be able to convert a fastq file to aln. Fastq files only contain the sequences and the quality of the read, no information about alignment. If you converted fastq to aln I would guess that this is your problem. You must first map your sequences to the genome, then you can convert that output to aln.
            Thanx for the detailed info. I think I may be able to fix it now bcos I took the original FastQ file and converted it into aln. I was under the assumption that since I provided the Rat genome (rn4) this program also does the alignment (similar to bowtie) and then calls the peaks. I will try now with the bowtie output. How do I convert the bowtie output to aln in that case? Sorry for all the newb questions :-)

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            • #51
              Originally posted by harishrk View Post
              Thanx for the detailed info. I think I may be able to fix it now bcos I took the original FastQ file and converted it into aln. I was under the assumption that since I provided the Rat genome (rn4) this program also does the alignment (similar to bowtie) and then calls the peaks. I will try now with the bowtie output. How do I convert the bowtie output to aln in that case? Sorry for all the newb questions :-)
              Try reading the manual.

              Comment


              • #52
                BRA file format

                I have BAM files after BWa alignments will it be compatible with Cis genome it says BRA format. How to get that format. I can convert BAM to SAM

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                • #53
                  Hi all,

                  I am using latest Cisgenome (windows version) to call Chi-seq peaks. But I got the errors when I used "Two sample peak calling (New and recommend)". After I added my IP and input file in aln format and used default setting, I got the error window "cannot write sample list to argument file!"

                  Would you tell me what the problem is ? I also tried the demo data, the same happened.

                  Thank you so much

                  Wei

                  Comment


                  • #54
                    Honey,

                    You can convert like this:

                    BAM -> BED -> ALN

                    Then use the ALN file with the peak calling to get a BAR file. I use the bedtools package to convert bam to bed and cisgenome to convert bed to aln.

                    Comment


                    • #55
                      yes dear, I am doing extactly the same

                      but cisgenome(windows version) seems not like my PC, so I switched to linux version on our cluster and it worked.

                      I wonder it might be a bug of windows version.

                      Originally posted by gntc View Post
                      Honey,

                      You can convert like this:

                      BAM -> BED -> ALN

                      Then use the ALN file with the peak calling to get a BAR file. I use the bedtools package to convert bam to bed and cisgenome to convert bed to aln.

                      Comment


                      • #56
                        Originally posted by townway View Post
                        yes dear, I am doing extactly the same

                        but cisgenome(windows version) seems not like my PC, so I switched to linux version on our cluster and it worked.

                        I wonder it might be a bug of windows version.
                        Haha, yes dear.

                        The windows version is buggy and annoying. Good to know that I'm not the only one doing what I'm doing and having problems with the windows version.

                        Comment


                        • #57
                          Does anyone know why when running One Sample Peak Calling Peak Detection with Boundary Refinement and Single Strand Filtering selected no .cod file is created? When I run this with my data I get 6 new files:

                          title.bar
                          title.cgw
                          title_F.bar
                          title_F.cgw
                          titlle_R.bar.tmp
                          title_R.regtmp

                          The .tmp files suggest to me that maybe the program is crashing. Has anyone else experienced this?

                          Comment


                          • #58
                            I agree cisgenome is probably created by a lInux reseacher and they never cared it has to be used by biologists. I wasted lot of time and end up using Cistrome they need to look into that. They even dont respond emails. That is bit annoying.... sorry but it is true.. If you can not support community then take off your software from public claims

                            Comment


                            • #59
                              Originally posted by ljul View Post
                              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.
                              Hi everybody, I just started using Cisgenome and was hoping to run it on my Mac using Parallels. However, I'm experiencing similar problems and was hoping anybody has a clue how to overcome this issue?

                              Cheers,

                              Bas

                              Comment


                              • #60
                                why not running it under OSX natively, i.e. Darwin??

                                Comment

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