miRPara for novel miRNA discovery

Question

[Rituriya]

Has anyone used the tool named 'miRPara' for novel discovery of miRNAs? It seems to be quite an old tool (last update 2013).

After a cumbersome installation of the tool, I am always getting zero miRNAs as output. I am a novice when it comes to dealing with novel miRNA discovery. I have tried miRDeep2 and have got a few novel miRNAs. Please share your experiences with this tool and other tools where you have successfully found novel miRNAs.

Thank you.

Answer 1

[Emilio Marmol]

There are several tools out there, but in my experience, many of them are difficult or imposible to use. Some of them are not available any more or are web based so they are quite limited.

miRDeep2 and Mirnovo are good options in my opinion, if you have smallRNAseq data. But their outputs can be quite hard to interpret and integrate.

I struggled with the same problem and decided to create my own tool for doing miRNA prediction, and we were able to validate some of the predicted new miRNAs by qPCR.

You can have a look and give it a try. Its a beta-version and paper will be sent soon for consideration.

Check it and if you have any doubts, do not hesitate to contact me:

http://www.github.com/emarmolsanchez/eMIRNA

[Rituriya]

Sure, I will give it a try. Thank you.