miR-PREFeR
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