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: http://paste.ubuntu.com/20905603/
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: http://paste.ubuntu.com/20906637/
The coding sequence for the predicted gene linked above (MDP0000134856) is found in one more reference file (.fa), which looks like this: http://paste.ubuntu.com/20906957/
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: http://paste.ubuntu.com/20907420/) 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.