RDI

A Fast Algorithm for Calculating a Novel Degradation Index from RNA-seq Data

Prerequisite

Before using RDI package, make sure you have installed python3 and the required modules: argparse, numpy, pandas, math, and random.

Install RDI

To install RDI, download the latest release RDI-RDIv1.0.0.tar.gz, then run

install.packages("RDI-RDIv1.0.0.tar.gz",repo=NULL,type="source")

Run RDI

To run RDI, first create and index the reference transcriptome for calculating RDI

create_index(fasta_file, output_prefix) # fasta file is the reference transcriptome, for example GRCm38 for mouse

Then calculate RDI value for each sample

calculate_RDI(fq_file1, fq_file2, index_path, num_threads, output_dir)