Question: Can anyone suggest me the pipeline for de novo prediction of miRNAs?
2
gravatar for harshraje19
6 months ago by
harshraje1930
harshraje1930 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 7 weeks ago by m.s_tabatabaei0 • written 6 months ago by harshraje1930

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

ADD REPLYlink written 6 months ago by Asaf8.3k

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 6 months ago by harshraje1930

is it 2x300 bp data?

ADD REPLYlink written 6 months ago by cpad011213k

Why would one need 300 bp data for miRNA?

ADD REPLYlink written 6 months ago by genomax87k

Ok. Thank you. I will try

ADD REPLYlink written 6 months ago by harshraje1930

Please comment on the answer instead of adding an answer

ADD REPLYlink written 6 months ago by Asaf8.3k

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

ADD REPLYlink written 7 weeks ago by m.s_tabatabaei0

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.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by genomax87k
1
gravatar for Asaf
6 months ago by
Asaf8.3k
Israel
Asaf8.3k wrote:

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

ADD COMMENTlink written 6 months ago by Asaf8.3k

ok ... Thank you Asaf

ADD REPLYlink written 6 months ago by harshraje1930

look at mirnovo and mipie as well.. @ harshraje19

ADD REPLYlink modified 6 months ago • written 6 months ago by cpad011213k
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