IUTA-1.0 in the Discovery Environment

Alert:

The iPlant App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01'). In critical cases, please report your concern to the iPlant Ask forum or to support@iplantcollaborative.org. Thank you for your patience.

The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to upendra@cyverse.org. Thank you.

Rationale and background:

IUTA: Isoform Usage Two-step Analysis

Liang Niu, Weichun Huang, David M Umbach and Leping Li. BMC Genomics 201415:862

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”.

Note

This tool only works will Illumina paired-end RNA-Seq data and no results w