miR-PREFeR 0.24

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

Quick Start

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