miRNA help

Question

[ver de terre]

Hi,

I am new to bioinformatics and need to do sequencing analysis on microRNA (≤ 50bp, after adaptor trimming) of a nematode, but the miRNAs aren’t known. Are there any good papers/resources people recommend to help with the analysis?

Also does anyone know a method of doing a plot of first nucleotide vs length (similar to https://www.researchgate.net/figure/Length-distribution-and-nucleotide-bias-of-the-detected-cucumber-miRNAs-A-Length_fig2_340180106 )?

Thanks.

[Buffo]

You can try miRdeep2, it was designed for analyzing known and unknown miRNAs, but be careful, mirRNA analysis is not a trivial task, I would recommend you to take a course/tutorials before starting such analysis.

Answer 1

[Apex92]

As Buffo mentioned, miRDeep2 is a suitable tool for this. You can run mapper.pl from miRDeep2 on your samples and do not forget to use the -d option that helps listing star and mature arms throughout all samples. If you find one RNA structure (in the pdf reports) similar to the canonical miRNA structure then you can go back to the report and see if both arms of that specific miRNA span throughout all samples - then this could be indicative of a potential miRNA.

Answer 2

[biofalconch]

Hi,

I really like the tool that Michael Axtell has developed for this purpose

https://github.com/MikeAxtell/ShortStack

It will give you those microRNAs that have a duplex like accumulation of reads, as well as their sequences. From there is just a simple Blast comparison against miRBase to see if they are similar to the ones already reported.

It is good to know that this can only be done if you have the genome sequence of your nematode, otherwise I would stick at a comparison with miRBase to find those that are conserved.