Question: Can anyone suggest me the pipeline for de novo prediction of miRNAs?
1
gravatar for harshraje19
4 days ago by
harshraje1910
harshraje1910 wrote:

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

ADD COMMENTlink modified 3 days ago • written 4 days ago by harshraje1910

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

ADD REPLYlink written 3 days ago by Asaf6.6k

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.

ADD REPLYlink written 3 days ago by harshraje1910

is it 2x300 bp data?

ADD REPLYlink written 3 days ago by cpad011212k

Ok. Thank you. I will try

ADD REPLYlink written 3 days ago by harshraje1910

Please comment on the answer instead of adding an answer

ADD REPLYlink written 3 days ago by Asaf6.6k
0
gravatar for Asaf
3 days ago by
Asaf6.6k
Israel
Asaf6.6k wrote:

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

ADD COMMENTlink written 3 days ago by Asaf6.6k

ok ... Thank you Asaf

ADD REPLYlink written 2 days ago by harshraje1910

look at mirnovo and mipie as well.. @ harshraje19

ADD REPLYlink modified 2 days ago • written 2 days ago by cpad011212k
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