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  • Galaxy -> cummeRbund How?

    Hi,

    I process my data using Galaxy due to the lack of good server, everything work fine Tophat->Cufflink->Cuffcompare->Cuffdiff (these files look fine)

    Problem starts when try to open them from R and I cannot force cummeRbund to load the files to db that I import from Galaxy, should I combine them somehow, or simply place in one directory.

    I would really appreciate your help.

    Best!

  • #2
    some more details...

    > cuff<-readCufflinks("~XXX/RNAseq/proteinA")
    Creating database ~XXX/RNAseq/proteinA/cuffData.db
    Reading ~~XXX/RNAseq/proteinA/genes.fpkm_tracking
    Checking samples table...
    Populating samples table...
    Writing genes table
    Reshaping geneData table
    Recasting
    Writing geneData table
    Error in sqliteExecStatement(con, statement, bind.data) :
    RS-DBI driver: (unable to bind data for parameter ':status')
    In addition: Warning messages:
    1: In `[<-.factor`(`*tmp*`, ri, value = c(0, 127890, 493903, 358.358, :
    invalid factor level, NAs generated
    2: In `[<-.factor`(`*tmp*`, ri, value = c(0, 127470, 481005, 262.821, :
    invalid factor level, NAs generated
    3: In `[<-.factor`(`*tmp*`, ri, value = c(0, 128310, 506801, 453.896, :
    invalid factor level, NAs generated
    4: In `[<-.factor`(`*tmp*`, ri, value = c(0, 886.049, 8123.86, 2.0214, :
    invalid factor level, NAs generated
    5: In `[<-.factor`(`*tmp*`, ri, value = c(0, 619.614, 0, 0, 11.9375, :
    invalid factor level, NAs generated
    6: In `[<-.factor`(`*tmp*`, ri, value = c(0, 1152.48, 4298850, 4.56339, :
    invalid factor level, NAs generated

    Comment


    • #3
      Hi,

      If you only tell readCufflinks the directory with the files from Galaxy, you will need to first make sure you rename all the files to the default names cuffdiff usually uses. My recommendation would be to instead specify each argument manually.

      Something like this
      Code:
       
      cuff <- readCufflinks(dir = "path/to/galaxy/output/",
                               dbFile = "output_database",
                               geneFPKM = "genes_fpkm_tracking",
                               geneDiff = "genes_exp",
                               isoformFPKM = "isoforms_fpkm_tracking",
                               isoformDiff = "isoforms_exp",
                               TSSFPKM = "tss_groups_fpkm_tracking",
                               TSSDiff = "tss_groups_exp",
                               CDSFPKM = "cds_fpkm_tracking",
                               CDSExpDiff = "cds_exp_diff",
                               CDSDiff = "cds_diff",
                               promoterFile = "promoters_diff",
                               splicingFile = "splicing_diff",
                               rebuild = T)
      Hope it helps,
      Carlos

      Comment


      • #4
        hi,

        Doubt clarification.

        what is that output_database ?

        Comment


        • #5
          hi all,
          can anyone tell em how to fix this?

          head(features(myGene))
          Error in function (classes, fdef, mtable) :
          unable to find an inherited method for function "features", for signature "CuffGene"


          thanks,
          ibseq

          Comment


          • #6
            Just found this thread as I had the same problem as above for:
            ...
            head(features(myGene))
            Error in function (classes, fdef, mtable) :
            unable to find an inherited method for function "features", for signature "CuffGene"
            ...
            and managed to find the cause

            The problem is if you load the library("GenomicFeatures") explicitly, to make a txdb object for example, it somehow stops the features(myGene) from working. The trick is to load CummeRbund, load GenomicFeatures, do what you need with the latter, then unload GenomicFeatures again. It will complain that it can't, but seems to fix the issue nonetheless.

            Using R 3.6.0 and BioConductor 3.9, in windows and CentOS Linux.

            --Ed

            Comment

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