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:
[email protected]
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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