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  • Cufflinks result

    Hi..~~

    I did cufflinks and as output, I had three files:

    -transcript.gtf
    -genes.fpkm_tracking
    -isoforms.fpkm_tracking

    My question is on genes.fpkm_tracking. As I understood, from column G, we can find out the location of the corresponding gene to the transcript which was found by cufflinks.

    For example: 1:161238-161297 => In my understanding, this means the transcript was transcribed from chromosome 1 from base pair number 161238 to base pair number 161297. Tell me if I am wrong.

    Then my supervisor asked me to find out a way to find the name of the gene (not only the chromosome and location on the chromosome but name of the gene) and not by searching in the google.

    Is there any way? Is there any tool?

    Thank you
    Last edited by Saeideh; 09-07-2015, 03:07 AM.

  • #2
    Hi Saeideh,

    I am new to Cufflinks myself, but when you look at the tracking file, the gene_id should be listed here as well (column D?). It certainly depends on which reference annotation file you've used, whther or not this name is descriptive.

    A nice alternative if to use the R package cummeRbund (same authors), which allows you to connect gene annotation data with you expression data.

    Maybe you could also use cuffcompare to assign transcripts to a reference annotation (it does far more, but in theory, you should also get the names assigned).

    Markus

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    • #3
      Hi Markus~

      Thank youuuu.. The time I asked the question, I did not know what is reference annotation file!! but now I know.
      and I used this command: cufflinks --GTF annotationfile.gtf accepted_hits.bam
      and I could get the result.
      Last edited by Saeideh; 09-08-2015, 12:37 AM.

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