Hello. I have a quick question about Cuffdiff analysis. 

I have obtained two SRA files and converted them to fastq files which were uploaded to Galaxy via FTP server. My analysis was followed by Fastq groomer, Tophat, Cufflinks, Cuffcompare, and eventually Cuffdiff. (Gene annotation was also downloaded from UCSC table browser in GTF format) I've downloaded gene differential expression testing, one of the output files of Cuffdiff, and viewed it in excel sheet. However, I have only zeros recorded for value_1, value_2, log2, test_stat and only ones recorded for p_value and q_value. 

Is it likely that I might have obtained wrong gene annotation file and caused this problem? 

Thank you 

Yona Kim

Department of Genetics 

Rutgers University - New Brunswick Campus