Hi Jennifer,
thanks for the advice.  you are right, I meant that the fpkm values are 0.
 I have checked the things you suggested, and everything matches up as far
as I can tell.  I will start over from the mapping and see if that helps.

On Mon, Jul 2, 2012 at 10:57 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:

> Hello Paul,
> By "null values" I am guessing that you mean that the FPKM values are "0".
> http://cufflinks.cbcb.umd.edu/**manual.html#transexpr<http://cufflinks.cbcb.umd.edu/manual.html#transexpr>
> This is an indication of a possible mismatch between the input BAM/SAM
> data and the reference annotation GTF file.  You will need to double check
> that both of these are true between all inputs:
> 1 - the chromosome naming is identical
> 2 - the sort ordering is identical
> Our RNA-seq FAQ has items that cover both:
> https://main.g2.bx.psu.edu/u/**jeremy/p/transcriptome-**analysis-faq<https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq>
> If that does not resolve the issue, and there is no error dataset from
> Galaxy, you might consider the Cufflinks help email address next:
> tophat.cuffli...@gmail.com
> http://wiki.g2.bx.psu.edu/**Support#Interpreting_**scientific_results<http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results>
> (see Example: unexpected results with RNA-seq analysis tools.)
> Best,
> Jen
> Galaxy team
>  I was hoping you could enlighten me about a problem I am currently
>>> having.  I have two rna-seq datasets that I am trying to evaluate using
>>> cufflinks - I keep getting null sets back with the second set, no matter
>>> what I do.  I am pretty sure that the data are identical in nature, just
>>> from different conditions.  Is there an issue with the current cufflinks
>>> instance?  Or am I screwing up somehow.  I am trying to evaluate item 149
>>> from my history (which is the filtered and sorted set from Bowtie
>>> analysis).  This should be identical in nature to item 113, with the only
>>> difference being the read source (same bug, different conditions).  Both
>>> were mapped to the same ref genome (from the history) and the same
>>> annotation file (again, from the history).  Any help is much appreciated!
>>> --
>>> Paul
> --
> Jennifer Jackson
> http://galaxyproject.org

Paul Orwin, Ph.D.
Associate Professor, Biology Department
California State University, San Bernardino
5500 University Pkwy
San Bernardino, CA, 92407
(909) 537-5405
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