miRNA Discovery

[Tanushree]

Dear All,
I am trying to make pipeline for denovo miRNA discovery so can anyone help with what can be probable methods for discovery of novel miRNA.

[patternist]

try miRdeep, it worked for me.

[Tanushree]

Thank you,
but can you tel me something in detail about miRdeep, i am fresher to this.
hoping for quick reply.

[NicoBxl]

http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/index.html

download the demo file, it's easy to use.

[steven]

Don't forget the seqanswers wiki.
For instance, looking for "mirna" gives you this.

[Tanushree]

I am trying out miRDeep, but what should i do in the case where reference genome is not available for mapping!!

[NicoBxl]

mmh you can try with a related species genome.

[waterboy]

Thank U
Yes, me trying it with related species. What are the necessary filterations required before using miRDeep. Please do reply!!!!

[waterboy]

Is this suitable for Solid reads.

[Tanushree]

I am done with the miRDeep , But how to interpret the prediction file, Especially identifying the novel miRNA

[NicoBxl]

You've a score for each prediction. Higher the score is, better it is.

[Tanushree]

Is miRDeep compatible with Solid reads? How to identify novel miRNA from predicted files.

[Bruins]

Have you read the mirDeep publication?

miRDeep
Deciphering the porcine intestinal microRNA transcriptome. (using miRDeep)
Another tool to find miRNAs in sequencing data:
MIReNA

[Tanushree]

Thank you,
Yes i have gone through its publication. I am having the solid reads and i want to discover novel mirna for which i used mirdeep and the python script to discover them. What is the percentage of its accuracy. Can tis results be considered further.

[NicoBxl]

miRDeep it's just a prediction tool. After that, you've to confirmed them experimentally ( custom RT-PCR stemloop per example )