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  • Replicates error in CummeRbund package in R

    Dear All,

    I am analyzing RNAseq data to study DEGs in two diffrent conditions. i don't have any replicate for my samples. tophat->cufflinks->cuffdiff pipeline is completed and now i want to plot graphs using cummeRbund. while creating a database using readCufflinks package i am getting following error.

    Creating database E:/cuff_out/cuffData.db
    Reading Run Info File E:/cuff_out/run.info
    Writing runInfo Table
    Reading Read Group Info E:/cuff_out/read_groups.info
    Writing replicates Table
    Error in sqliteSendQuery(con, statement, bind.data) :
    rsqlite_query_send: could not execute: UNIQUE constraint failed: replicates.rep_name


    Can anyone please help me to solve this.?

  • #2
    What is the content of E:/cuff_out/read_groups.info?
    What command was used to run Cuffdiff?
    Also, perhaps not necessary, were there any error messages during the Cuffdiff run?

    Comment


    • #3
      thank for your reply blancha

      Read_groups.info contains...

      file condition replicate_num total_mass norm_mass internal_scale external_scale
      control_tophat_out/accepted_hits.bam control 0 3.25226e+07 3.85494e+07 0.83201 1
      test_tophat_out/accepted_hits.bam treated 0 4.569e+07 3.85494e+07 1.20191 1

      cuffdiff was run with default command. along with two accepted_hits.bam file, human genome reference and GTF was there as input. i also used -u (rescue method for multi-reads.

      cuffdiff was completed successfully.

      Comment


      • #4
        Sorry, I don't know the answer.
        Looks correct to me.
        Other than suggesting to update CummeRbund If you have an ancient version, older than 2.7.3, I don't have any solutions to propose to this specific problem.

        Comment


        • #5
          thank for your reply blancha

          Comment

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