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Getting Bowtie to work



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  • Getting Bowtie to work

    I installed bowtie from the sourceforge website, I unzipped it in a unix shell in windows, and when I try typing "make" inside of the newly made folder, there is an error saying it expects 2 more arguments. I've tried sound dis2unix for all files and I've tried it without it. Thank you for your help.

  • #2
    the error message is:

    make: *** No targets specified and no makefile found. Stop.


    • #3
      I'm using Win32 version After unzipping I typed:

      ./bowtie.exe e_coli reads/e_coli_1000.fq

      and the results are:

      x11drv: Can't open display:
      Please ensure that your X server is running and that $DISPLAY is set correctly.

      How can I fix this?


      • #4
        are you trying to use a bowtie.exe on a linux system?

        You are probaly using the iTunes bowtie on a linux system.

        Did you get bowtie from http://bowtie-bio.sourceforge.net/index.shtml?


        • #5
          Yes, I downloaded it from that website, and i'm using a unix shell in windows.


          • #6
            Well, linux has no .exe extensions. So trying to use that .exe bowtie will never work. You should get a linux version to run in your linux shell.


            • #7
              sortFiles problem

              Hi , Can anyone help me with this problem please.
              I have bowtie aligned seq and trying to convert it into wigfiles using the findpeak.
              so I performed a SeparateReads and saved it in a folder as per the manual.When I tried using the SortReads on the gz file in the separatereads...I get an error saying : java : no match....
              I do have the java jre path set and it worked for the separatereads..
              Is it that I need to unzip the gz file and perform it?
              Any help? THanks


              • #8
                Sort files

                Ohk I got to work the sort files on my separate files to run! But it went out of memory!!!
                Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
                Any suggestion on how to fix this problem?


                • #9
                  If I used the SeparateReads from findpeaks directly on GERALD.export files ,specifying the -aligner eland, I get an error message: Any help?
                  Version: Initializing class SeparateReads $Revision: 1082 $
                  Version: Initializing class Log_Buffer $Revision: 1145 $
                  Version: Initializing class Generic_AlignRead_Iterator $Revision: 1318 $
                  Version: Initializing class ElandIterator $Revision: 841 $
                  Error: Error processing mistmatch type 7 on line 1of Eland file


                  • #10
                    Did you try using eland_extended?
                    __ you probably solved this, so I wish I could remove my post


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