Hi all, 

I am attempting to use tophat>cufflinks>cuffmerge>cuffdiff to compare 
transcript expression in 3 samples (no replicates, illumina single-end reads). 
Using the built in UCSC mm9 reference genome I can complete the analysis just 
fine, with the caveat that there is no annotation.

When I repeat the analysis using the illumina igenome UCSC mm9 .gtf annotation 
file I get the following error in Cufflinks:

An error occurred running this job: cufflinks v1.3.0 
cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G 
/galaxy/main_pool/pool5/files/004/309/dataset_4309547.dat -N
Error running cufflinks. 
return code = -11
cufflinks: /lib64/libz.so.1: no version information available

I have set the identifier/build as "Mouse July 2007 (NCBI37/mm9) (mm9)" so that 
does not seem to be the probelem. Suggestions as to how to amend this problem 
OR add annotations to the already completed analysis would be terrific.



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