How to get a hg38 miRNA annotation file work in galaxy?

Question: How to get a hg38 miRNA annotation file work in galaxy?

3.8 years ago by

United States

Hi,

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?

Thanks,

Yalu

rna-seq galaxy • 1.5k views

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modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by natalie022487 • 0

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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:
http://cole-trapnell-lab.github.io/cufflinks/manual/

And we have a live RNA-seq tutorial here on the public Main instance:
http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise

Additional RNA-seq tutorials can be found in our wiki on the Learn page:
http://wiki.galaxyproject.org/Learn#Other_Tutorials

Best, Jen, Galaxy team

ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

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:
https://toolshed.g2.bx.psu.edu/view/rnateam/mirdeep2_mapper
https://toolshed.g2.bx.psu.edu/view/rnateam/mirdeep2_quantifier
https://toolshed.g2.bx.psu.edu/view/david-hoover/mirdeep2_and_targetspy_dh

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

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