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.
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Plant Physiol. 2013 Jul;162(3):1750-63. doi: 10.1104/pp.113.217778. Epub 2013 Jun 4.
Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots.
Li W, Lin WD, Ray P, Lan P, Schmidt W.