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  • get FPKM for Ensembl Gene IDs

    Hi all:

    I am trying to run tophat + cufflink to get FPKM values.

    my question here is:
    how to use Ensembl Gene IDs, instead of the default cufflinks Gene IDs (e.g. CUFF.1), to represent the results ?

    my procedure is rather simple:
    1. tophat mm9 SRR306857.fastq
    2. cufflinks accepted_hits.bam

    What kind of reference file I should add to these computation to get FPKM value for Ensembl Gene IDs?

    Thanks in advance!
    Best,

  • #2
    Just download the GTF and use the -G option.

    Comment


    • #3
      Thank you!

      I have used the genes.gtf from NCBIM37, which result in 0 FPKM.
      I guess that since I have used mm9 in my Tophat, I should also use mm9-based genes.gtf in my cufflinks?
      Is that right?

      Thanks in advance!
      Best,

      Comment


      • #4
        Here is the mm9 GTF file from Ensembl: ftp://ftp.ensembl.org/pub/release-60/gtf/mus_musculus/

        NCBI37 = mm9 build

        Comment


        • #5
          Thank you!
          I will give a try!

          Comment

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