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


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