miRDeep2 2.0.0.8 quantifier
miRDeep2 2.0.0.8 quantifier
This app maps deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs.
Quick Start
- To use miRDeep2 2.0.0.8 quantifier, provide sequencing reads, known miRNAs sequences and known precursor sequences for your species of interest.
- Resources: https://github.com/rajewsky-lab/mirdeep2/tree/master/tutorial_dir
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> miRDeep2
Input File(s)
reads_collapsed.fasta
mature_ref_this_species.fa
precursors_ref_this_species.fa
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.
Leave all parameters as default.
Output File(s)
For the test case, the output file you will find in the example_data directory is miRNAs_expressed_all_samples_1532534506.csv