miR-PREFeR 0.24

This app runs the miR-PREFeR pipeline. MiR-PREFeR predicts miRNA from small RNAseq data.

Quick Start

To use miR-PREFeR 0.24, provide a reference genome in FASTA format, one or more SAM alignment files and miR-PREFeR config file
Resources: https://github.com/hangelwen/miR-PREFeR

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> miR-PREFeR

Input File(s)

TAIR10.chr1.fa (genome FASTA)
cold.chr1.sam
pdep.chr1.sam
pind.chr1.sam
TAIR10.chr1.CDS.gff (GFF exclude)

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Add config.example.de to the config file field.

Leave all other parameters as default.

Output File(s)

failed_readmapping (folder)
miRNA.stat.txt
readmapping (folder)
TAIR10-example_failed.dict.dump
TAIR10-example.log
TAIR10-example_miRNA.detail.csv
TAIR10-example_miRNA.detail.html
TAIR10-example_miRNA.gff3
TAIR10-example_miRNA.mature.fa
TAIR10-example_miRNA.precursor.fa
TAIR10-example_miRNA.precursor.ss
TAIR10-example_reason_why_not_miRNA.txt

Tool Source for App

https://github.com/hangelwen/miR-PREFeR