RACKJ

RACKJ (Read Analysis & Comparison Kit in Java) is a set of Java programs that analyze and compare RNA-seq data made by NGS (Next-Generation Sequencing) technologies. In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing events. In so doing, it is feasible to compare two samples and identify genes with most significant difference in exon(splicing)-level.

Documentation

Flowchart
An Example for RNAseq Analysis
Manual
Useful Scripts
Scripts for Mapping
Add-On Scripts

Download

The latest release of RACKJ is available at the download area of the RACKJ project.
RACKJ uses a very simple format to record gene locations and exon ranges. You may use the CanonicalGFF program (see here for example) or the SeqGeneMd program to generate a .cgff file and a .model for yourself. You may also download prebuild .cgff and .model files.

Contact

Please raise an issue at here if you have any questions.