Worklow for miRNA prediction in plants

Question

[bartosz.kozak]

Hi there!

I have small RNA data-set which I want to analyzed. I don't have much experience in this field, so I try to find information about those type of analysis. Many people suggest usage of miR-PREFeR for predicting miRNA in plants. My question is if workflow I'm planing to usage in analysis is correct or should I change some steps.

1. Prepare fastq data acording to miR-PREFeR tutorial
2. Run miR-PREFeR with default parameters using files form step 1
3. Use RNA databases (miRBase, Rfam, RNACentral) and BLAST to find know miRNA and false positives (siRNA, most of 24 nt predictions) in miR-PREFeR results.
4. Discard false positives (siRNA)
5. Use known and novel miRNA predicted by miR-PREFeR in downstream analysis

Is there other way to filter results from miR-PREFeR for discard false positives?

Thanks, Bartek