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

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

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
(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



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