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  • Question on QuEST

    Hello, all.

    I am trying to process our ChIPseq data using QuEST.


    I have managed to compile the program and succeeded in processing the sample data on the homepage above.
    However, when I tried to do the same thing with our data, QuEST displays errors and I cannot process the data.

    Below is several lines of our data,
    GGTGCCCTGCTTCCTTGCCATTCCAGCCATGCCTGA 0 0 chr6:136088939 F
    GTTTAGCAGTGGTTCCAGAGGACTTAATAGACAGAA 0 0 chr6:43415552 F
    TAAACTCTTACAACCTAAAGCTCTAAGTCCTTAGGA 0 0 chr13:86619993 F

    and this is the error that I keep getting.
    . Skipping.pected +/- for orientation of read but found F
    . Skipping.pected +/- for orientation of read but found F
    . Skipping.pected +/- for orientation of read but found F

    What is wrong with our data? I hope some of you can help us out.
    Thanks in advance.

  • #2
    Originally posted by kopo3 View Post
    Hello, all.

    I am trying to process our ChIPseq data using QuEST.


    I have managed to compile the program and succeeded in processing the sample data on the homepage above.
    However, when I tried to do the same thing with our data, QuEST displays errors and I cannot process the data.

    Below is several lines of our data,
    GGTGCCCTGCTTCCTTGCCATTCCAGCCATGCCTGA 0 0 chr6:136088939 F
    GTTTAGCAGTGGTTCCAGAGGACTTAATAGACAGAA 0 0 chr6:43415552 F
    TAAACTCTTACAACCTAAAGCTCTAAGTCCTTAGGA 0 0 chr13:86619993 F

    and this is the error that I keep getting.
    . Skipping.pected +/- for orientation of read but found F
    . Skipping.pected +/- for orientation of read but found F
    . Skipping.pected +/- for orientation of read but found F

    What is wrong with our data? I hope some of you can help us out.
    Thanks in advance.
    I am wondering if you used the option -solexa_align_ChIP followed by your input file.
    Xi Wang

    Comment


    • #3
      Thanks for the reply.

      Originally posted by Xi Wang View Post
      I am wondering if you used the option -solexa_align_ChIP followed by your input file.
      Dear Wang.

      Thank you for your quick reply.
      Actually, the command line I used was,

      ./generate_QuEST_parameters.pl -solexa_align_ChIP ./data_file.txt -gt ./genome_table -ap ./QuEST_analysis -ChIP_name DBF_CELL

      Curiously, when I carried the command out in a cygwin environment, I did not encounter this error, although in the latter part of the process, the program ceased to work due to another error.
      However, when I carried it out on a 64bit Fedora9 environment (in which I was successful in processing the sample file on the original homepage) I got this error.
      Do you have any idea what is wrong with the data, or command line?

      Comment


      • #4
        Originally posted by kopo3 View Post
        Dear Wang.

        Thank you for your quick reply.
        Actually, the command line I used was,

        ./generate_QuEST_parameters.pl -solexa_align_ChIP ./data_file.txt -gt ./genome_table -ap ./QuEST_analysis -ChIP_name DBF_CELL

        Curiously, when I carried the command out in a cygwin environment, I did not encounter this error, although in the latter part of the process, the program ceased to work due to another error.
        However, when I carried it out on a 64bit Fedora9 environment (in which I was successful in processing the sample file on the original homepage) I got this error.
        Do you have any idea what is wrong with the data, or command line?

        That is quite abnormal. Waiting for the author to answer...

        Days ago, I also encountered an error when running QuEST 2.4. I think it would be a common problem. So I post it here.

        I found that in the file "run_QuEST_with_param_file.pl": Line 742
        my $pseudo_ChIP_scores_path = $scores_path . "/pseuod_ChIP";

        there is a misspelling: "/pseudo_ChIP" instead of "/pseuod_ChIP".

        This misspelling will cause the program stoped with an error message:
        >> bad file name: ./scores/pseudo_ChIP/chr1.score
        >> run_generate_profile_with_param_file.pl: Caught an error message (code 256), passing error message to the top script.
        >> run_QuEST_with_param_file.pl: Caught an error message (code 768) when running generate_pseudo_ChIP_profile. Aborting.
        Last edited by Xi Wang; 10-30-2009, 10:21 PM.
        Xi Wang

        Comment


        • #5
          The original file that I had was an eland-extended file.
          I converted the file so that it was similar to the example file.
          I noticed that I could use an option so that QuEST can analyze eland-extended files and it worked!
          So, although I still do not know why QuEST could not handle the file I converted, it seems that I can use QuEST to analyze files that we have.

          Thank you!

          Comment


          • #6
            Hi kopo3, my guess is that the solexa align file is messed up in some way, e.g. has tab as a separator instead of a space.

            Xi, thanks for catching the pseudo_ChIP typo - I had fixed this bug and posted a new version on my web site:


            Here's the direct link:


            Very best! Anton.
            Last edited by Anton; 11-03-2009, 01:06 PM.

            Comment


            • #7
              Problem using quest with illumina 1.3+ files

              Hi,
              What is the option for using eland_extended files as input? I have alignment files of the latest format (1.5.1 pipeline version). They look like this :
              R2D2 1 5 12 894 524 1 AGAGAGCAGGCTGAGACTACTAGGTGTGGGCAT eegggefgggfegeggggf`gTLTLITNPRSff chr10 3002722 F 3C29 55
              R2D2 1 5 31 1197 1453 1 AGAGAGCAGGCTGAGACTACTAGGTGTGGGCAT ggggggdgghegcggghggfggegcgfdgc chr10 3002722 F 3C29 57

              It doesn't seem to be recognized in default mode. From the manual I have, something different is expected. I can reformat the files to extract the info, but if there's an option already there, it'd be so much easier.

              Comment


              • #8
                Folks, please post your questions regarding QuEST into the QuEST Google group:



                It is much easier for me to handle questions there.
                Much appreciated!
                Best, Anton.

                Comment


                • #9
                  Hi all,
                  Do anyone has experience with Quest for chipseq data analysis. anyone can suggest how to use eland alignment files(export/sorted). however i tried and met some errors as posted above.
                  thanks in advance

                  Comment

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