Question: How can cufflinks/cuffdiff output be used when there are no gene_short_name's or meaningful gene_id's ?
gravatar for mattjames
2.8 years ago by
mattjames0 wrote:

I'm running RNA-Seq data through the tuxedo suite, and after running cufflinks (v 2.1.1) with the -g option to the annotated reference, the output files (e.g. genes.fpkm_tracking) start out like this:

None of the lines have a gene_short_name and all of the tracking_id's and gene_id's are "cuff.#". So the locus (e.g. MDC000002.325:1805-3635) seems to be the way to find more info about these sequences, and indeed it's listed in the reference .gff like this:

The coding sequence for the predicted gene linked above (MDP0000134856) is found in one more reference file (.fa), which looks like this:

So, I'm wondering two things at this point. First, after I've done the cuffmerge / cuffdiff steps and end up with similar info as in the genes.fpkm_tracking file (see here: i.e. no gene names, just the loci, how do I turn those loci into something meaningful? I have approx. 1450 genes significantly differentially expressed among my samples, but all I have is a list of XLOC #'s or locus values. And second, as I was typing this question up I realized that in the first link it shows the one sample with a FPKM of 0.0584575 for the MDC000002.325:1805-3635 locus, but in the last link whichi s the cuffdiff output it shows FPKM's of 0 for all 4 samples compared... why would that be happening??

Thank you so much for any help you can offer.

ADD COMMENTlink modified 22 months ago by Suryawanshi Padmaja0 • written 2.8 years ago by mattjames0
gravatar for Suryawanshi Padmaja
22 months ago by
India/Dharwad/University of Agricultural Sciences/Institute of Agri-Biotechnology(IABT)
Suryawanshi Padmaja0 wrote:

I had a similar problem of not getting appropriate gene ID in my cuffdiff output; check the following post;

How to retrieve gene ID, gene description, after cuffdiff analysis[1]

may be the suggestions given therein could be of help to you

ADD COMMENTlink modified 22 months ago • written 22 months ago by Suryawanshi Padmaja0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 783 users visited in the last hour