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  • cuffmerge - from wrong not indexed files?

    hi Everyone,
    I am new in RNAseq analysis. I have run tophat then cufflinks, and now I wnat to run cuffmerge, but I have found this problem:

    # cuffmerge -p 4 -g /path/to/genes.gtf -s /path/to/genome.fa /path/to/assemblies.txt

    [Thu Oct 23 13:18:51 2014] Beginning transcriptome assembly merge
    -------------------------------------------

    [Thu Oct 23 13:18:51 2014] Preparing output location ./merged_asm/
    Traceback (most recent call last):
    File "/usr/bin/cuffmerge", line 580, in <module>
    sys.exit(main())
    File "/usr/bin/cuffmerge", line 530, in main
    transfrag_list_file = open(args[0], "r")
    IOError: [Errno 2] No such file or directory: '/home/michalina/BAM_SAM_tophat_samtools/TS2/assemblies.txt


    I have no idea what is going wrong. My cufflinks were wrong? gtf or fa references file are not appropriate? hese are the same reference files that I use for previous analysis (tophat, cufflinks).

    many thanks for any commnet or advise
    M.

  • #2
    Have you made a list of the GTF files from your cufflinks assemblies and then put the names in the "assemblies.txt" file? Your error is about this file not being present.

    From Cuffmerge help:

    <assembly_list.txt> Text file "manifest" with a list (one per line) of GTF files that you'd like to merge together into a single GTF file.

    Comment


    • #3
      Hi Genomax,

      no I haven't, how can I do this? could you tell me?

      I did something like this:
      cat /home/michalina/BAM_SAM_tophat_samtools/TS/transcripts.gtf /home/michalina/BAM_SAM_tophat_samtools/TS2/transcripts.gtf > asseblies.txt

      but I was afraid it was wrong.

      Honestly, I am new one in all these things...

      Comment


      • #4
        Make a file called "assemblies.txt" and put these two lines in it (use a text editor):

        /home/michalina/BAM_SAM_tophat_samtools/TS/transcripts.gtf
        /home/michalina/BAM_SAM_tophat_samtools/TS2/transcripts.gtf

        Comment


        • #5
          wow! many thanks!!! that was that much simple

          Comment

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