miRDeep-P: getting the scripts to work

[all_your_base]

Hi all,

I've been playing with miRDeep-P recently, and have trouble even getting started. In particular, their script fetch_extended_precursors.pl is completing within a couple of seconds and returns no output.

This scripts takes the genome reference file and the miRNA .gff file and extends the precursors by 500nt up and downstream from the annotated site. I could write my own to accomplish this, but would like to use the miRDeep-P package as a whole the first time through.

If anyone has had similar experiences, please let me know!

[csmatyi]

we got it to run

We got the whole pipeline to run. Did you use an appropriate gff file and genome sequence file? What species are you studying? Maybe they have an appropriate species gff file for you on the mirdeep website.

[Latifa77]

hi,
did you get good results employing mirdeep-p?

[jack84]

Another tool for plant miRNA prediction: https://github.com/hangelwen/miR-PREFeR .