Can anyone suggest me the pipeline for de novo prediction of miRNAs?

Question

[harshraje19]

Dear All,

I am performing the miRNA prediction analysis. I am working on plant and genome of that plant species is available but miRNA sequence file is not there in mirbase. So I cannot predict the mirnas using miRDeep2 (I guess).

Can anyone suggest me any alternative pipeline for de novo prediction of plant miRNAs?

Thank you

[Asaf]

Do you have sRNA seq data or de-novo from genome?

[harshraje19]

i have small RNA seq data. I want to find out the miRNAs. The genome of that plant is available but miRNAs are not annotated and no miRNAs in mirbase database.

I want to go for de novo prediction of miRNAs.

[cpad0112]

is it 2x300 bp data?

[GenoMax]

Why would one need 300 bp data for miRNA?

[cpad0112]

@ genomax

1. https://www.frontiersin.org/articles/10.3389/fpls.2016.02058/full
2. http://www.plantcell.org/content/plantcell/early/2018/01/17/tpc.17.00851.full.pdf
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5868703/ (Table 1)

[harshraje19]

Ok. Thank you. I will try

[Asaf]

Please comment on the answer instead of adding an answer

[m.s_tabatabaei]

Hi Harshraje,

I have the same problem as your problem. I am working on small RNA data on plant in which there isn't any annotated reference genome for it. Could you please let me know if you got your answer. I am so thankful if you let me know which pipeline and tool you found to be good for plant small RNA seq?

thank you, Mina

[GenoMax]

m.s_tabatabaei : You have been asking this question for a while in various threads. Have you not been able to use the tools that have been posted in these various threads? There are papers linked in this thread that you should look at.

There is probably no definitive answer for your question. Was your data generated by a specific miRNA kit? If so, follow the instructions for that kit to clean/prep your data before you try doing alignments.

Answer 1

[Asaf]

You can try mirpea like used here: https://www.mdpi.com/1422-0067/19/5/1431/htm

[harshraje19]

ok ... Thank you Asaf

[cpad0112]

look at mirnovo and mipie as well.. @ harshraje19