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. Thanks! Sarah