[galaxy-user] Mapping miRNA data

Dear All I am interested in using Galaxy to compare miRNA sequencing data. I have previously groomed, clipped and then mapped miRNA data onto hg19 using bowtie. I have then identified differentially expressed miRNAs using cuffdiff and the UCSC downloaded miRNA/snoRNA database. However, I have recently tried to repeat this process but find the cuffdiff is unable to run. I just wondered why cuffdiff is no longer working or if there is alternative approach to comparing miRNA expression? Best wishes Mark