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  • ngsplot errors and questions

    I tried to find any similar questions but I couldn't

    So, I'm under ubuntu 14.04 64bit 32GB memmory

    First
    is the installation of ngsplot, I followed the guide as it is described (https://code.google.com/p/ngsplot/) for the installation.
    2. Add ngsplot executables to your PATH. Under bash, add line like this:

    export PATH=~/software/ngsplot/bin:$PATH

    to your ~/.bash_profile

    3. Set environment variable NGSPLOT like this in your ~/.bash_profile:

    export NGSPLOT=~/software/ngsplot

    Then in the terminal, execute:

    . ~/.bash_profile


    as I found out, there is no .bash_profile in my system
    second, if I open a new terminal window the system forgets all the paths... the same happens when I restart the system.

    so I have to repeat the PATH commands each time.

    Is there anythin I can do to make things a little bit more persistent?


    Second
    I'm using the following command line, but I got an error of unrecognized option

    ngs.plot.r -G hg18 -R enhancer -C ~/ngsplot/test.txt -O plottest.enchancer

    and I got the following error:

    Loading R libraries.....Done
    Configuring variables...Error in setupVars(args.tbl, default.tbl) :
    Unknown region specified. Must be one of: cgi exon genebody tss tes bed
    Execution halted
    third


    And finally...what is with the following message?

    In headerIndexBam(bam.list) :
    Aligner for: /media/trotos/4TB/WORK/archive/a_60min.sorted.bam cannot be determined. Will automatically convert mapping scores of 255.

    \third
    ngs.plot.r -G hg18 -R bed -E '/media/trotos/4TB/WORK/UCSC/hg18/wgEncodeBroadHmmHuvecHMM.bed' -C ~/ngsplot/SMAD7.txt -O plotSMADstest.Hmmm
    Loading R libraries.....Done
    Configuring variables...Error in file(file, "rt") : cannot open the connection
    Calls: SetupPlotCoord -> ReadBedCoord -> read.table -> file
    In addition: Warning messages:
    1: In ReadBedCoord(ur) : File name: '-1' does not seem to a correct name
    for bed file.

    2: In file(file, "rt") : cannot open file '-1': No such file or directory
    Execution halted
    trotos@UbuStupid:~$ ngs.plot.r -G hg18 -R bed -E '/media/trotos/4TB/WORK/UCSC/hg18/wgEncodeBroadHmmHuvecHMM.bed' -C ~/ngsplot/SMAD.txt -O plotSMADstest.Hmmm
    Loading R libraries.....Done
    Configuring variables...Error in file(file, "rt") : cannot open the connection
    Calls: SetupPlotCoord -> ReadBedCoord -> read.table -> file
    In addition: Warning messages:
    1: In ReadBedCoord(ur) : File name: '-1' does not seem to a correct name
    for bed file.

    2: In file(file, "rt") : cannot open file '-1': No such file or directory
    Execution halted
    the file is

    /media/trotos/4TB/WORK/archive/a0min.sorted.bam -1 "a0min"
    /media/trotos/4TB/WORK/archive/a30min.sorted.bam.bam -1 "a30min"
    /media/trotos/4TB/WORK/archive/a60min.sorted.bam.bam -1 "a60min"
    /media/trotos/4TB/WORK/archive/b0min_BWA-mem.sorted.bam -1 "b0min"
    /media/trotos/4TB/WORK/archive/b30min.sorted.bam.bam -1 "b30min"
    /media/trotos/4TB/WORK/archive/b60min.sorted.bam.bam -1 "b60min"
    /media/trotos/4TB/WORK/archive/c0min.sorted..bam -1 "c0min"
    /media/trotos/4TB/WORK/archive/c30min.sorted..bam -1 "c30min"
    /media/trotos/4TB/WORK/archive/c60min.sorted..bam -1 "c60min"
    /media/trotos/4TB/WORK/archive/d0min.sorted..bam -1 "d0min"
    /media/trotos/4TB/WORK/archive/d30min.sorted..bam -1 "d30min"
    /media/trotos/4TB/WORK/archive/d0min.sorted.bam -1 "d60min"
    Thank you for your time
    Last edited by trotos; 05-07-2014, 12:20 AM.

  • #2
    Hi Trotos,

    I can only help you with your first problem, as I'm not familiar with ngs.

    Depending on your distribution the .bash_profile may be called .profile only. Try to look in your home for such a file using "ls -an".

    If you use the export line in the terminal it is only available in that specific terminal, this is normal. When you use a variable in one terminal, it will also not be visible in other ones.

    When you have found your .profile file, add the following to the end of your file

    export PATH=$PATH:~/software/ngsplot/bin
    export NGSPLOT=$NGSPLOT:~/software/ngsplot

    (although I think it would also work without the "export")

    You will have to log out, log in again to make it working.

    Comment


    • #3
      Hi trotos,

      I am one of the authors of ngs.plot.
      For the second problem, ngs.plot doesn't support enhancer annotation of hg18. You may use hg19.
      For the third problem, the format of the configuration should be like this:
      /media/trotos/4TB/WORK/archive/a0min.sorted.bam /media/trotos/4TB/WORK/UCSC/hg18/wgEncodeBroadHmmHuvecHMM.bed "a0min"

      So in this way ngs.plot could be configured in a more flexible way.

      PS, if you have questions about ngs.plot, you are welcome to raise the questions in our google discussion forum. It is:

      Comment


      • #4
        Originally posted by WhatsOEver View Post
        Hi Trotos,

        I can only help you with your first problem, as I'm not familiar with ngs.

        Depending on your distribution the .bash_profile may be called .profile only. Try to look in your home for such a file using "ls -an".

        If you use the export line in the terminal it is only available in that specific terminal, this is normal. When you use a variable in one terminal, it will also not be visible in other ones.

        When you have found your .profile file, add the following to the end of your file

        export PATH=$PATH:~/software/ngsplot/bin
        export NGSPLOT=$NGSPLOT:~/software/ngsplot

        (although I think it would also work without the "export")

        You will have to log out, log in again to make it working.
        I fixed this one, I needed to enter something like the following to the very end of ~/.bashrc and only there. anything else didn't work or the system failed to login.


        export PATH=/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/sbin:/usr/bin:/bin
        #export PATH=/media/trotos/documents/NGS_programms/skewer:$PATH
        export PATH=~/ngsplot/bin:$PATH
        export NGSPLOT=~/ngsplot
        export PATH=/media/trotos/documents/NGS_programms/bwa-0.7.8/:$PATH
        export PATH=/media/trotos/documents/NGS_programms/bedtools2-2.19.1/bin:$PATH
        export PATH=/media/trotos/documents/NGS_programms/MACS2-2.0.10.20131216/bin:$PATH

        Comment


        • #5
          Originally posted by ishmael View Post
          Hi trotos,

          I am one of the authors of ngs.plot.
          For the second problem, ngs.plot doesn't support enhancer annotation of hg18. You may use hg19.
          For the third problem, the format of the configuration should be like this:
          /media/trotos/4TB/WORK/archive/a0min.sorted.bam /media/trotos/4TB/WORK/UCSC/hg18/wgEncodeBroadHmmHuvecHMM.bed "a0min"

          So in this way ngs.plot could be configured in a more flexible way.

          PS, if you have questions about ngs.plot, you are welcome to raise the questions in our google discussion forum. It is:
          http://groups.google.com/group/ngsplot-discuss
          Is there any way to annotate the enchancers???
          I will really need this answer.

          Comment


          • #6
            Originally posted by trotos View Post
            Is there any way to annotate the enchancers???
            I will really need this answer.
            If you want enhancers on hg18, you may need to generate an enhancer annotation in bed format yourself.
            Download the enhancer annotation from encode project, and then use liftover of UCSC to convert the coordinations from hg19 to hg18, and then feed this bed to ngsplot, it should work.

            Comment

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