Question: How to get a hg38 miRNA annotation file work in galaxy?
gravatar for natalie022487
3.8 years ago by
United States
natalie0224870 wrote:


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?



rna-seq galaxy • 1.5k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.8 years ago by natalie0224870
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Are you running Cufflinks and then CuffMerge in order to add any novel transcripts in your data to the existing reference annotation, before running Cuffdiff? If not, then any data in your samples - that is not represented in the reference annotation - will not be utilized by Cuffdiff.

The basic protocol is here:

And we have a live RNA-seq tutorial here on the public Main instance:

Additional RNA-seq tutorials can be found in our wiki on the Learn page:

Best, Jen, Galaxy team

ADD COMMENTlink written 3.8 years ago by Jennifer Hillman Jackson25k

I could mention that there are tools specifically for miRNA analysis in the tool shed. These may be more appropriate to your needs than the Tuxedo pipleline. Please see these links:

ADD REPLYlink written 3.8 years ago by Jennifer Hillman Jackson25k
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