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

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