I just started to use galaxy to analyze our NGS data, so I'm not good at it. My purpose is to know the differential expression level of MiRNAs in each sample. In order to achieve that, I ran Tophat2 against hg38, followed by Cuffdiff. However, Cuffdiff only allows me to run with an annotation file, but I could not find a MiRNA annotation file for hg38 from UCSC site. So I downloaded the gff3 annotation file from miRBase, and revised it myself according to the format of hg19 MiRNA annotation file from UCSC. I am able to use the new annotation file in Cuffdiff, but it works only to some extent, means for some MiRNAs, it gives the correct reads, but for others, it shows 0 (But there are hits at the exact location).
So does anyone have any idea what's going on with my annotation file? Or is there any suggestion of where to get the correct MiRNA annotation file for hg38?