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IUTA is an analysis tool of Illumina paired-end RNA-seq data for detecting differential usage of gene transcript isoforms. It first uses the EM algorithm to identify the usage of transcript isoforms for each gene, then tests the difference in the isoform usage between two groups based on the method for composition data analysis. IUTA takes RNA-Seq alignment files (in BAM format) from two groups of samples, together with a gene annotation file (in GTF format) for the related species, to test for differential isoform usage (set of relative abundances of isoforms) for each of the inquired genes. It outputs two tab-delimited files (with header): “estimates.txt” and “p_values.txt”.



 This tool only works will Illumina paired-end RNA-Seq data and no results will be generated from Illumina single end RNA-Seq data.