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PHASIS: a computational suite for de novo discovery and characterization of phased, siRNA-generating loci and their miRNA triggers

version : v3
updated : 04/17/2017
download: latest release

PHASIS is the "first" toolset for discovery and in-depth characterization of phased siRNAs clusters. It consists of three user accessible components that enables discovery of phased siRNA loci from tens to hundreds of sRNA libraries, performs quantification, annotation, and comparison of PHAS summaries between libraries from different treatments or stages or tissues, and finally identifies miRNA triggers of these PHAS loci. PHASIS provides several output files, and these are described in detail in tool-specific sections. The three PHASIS components are:

1. phasdetect: Identifies library-specific phased-loci, prepares and organizes the ancillary data.

2. phasemerge: Summarizes the libraries-specific results to a non-overlapping genome- or transcriptome-level set, quantifies phased siRNAs, annotates the PHAS loci by matching to genome annotations or transcriptome GTF and facilitates comparison of PHAS summaries.

3. phastrigs: Identifies miRNAs triggers for PHAS loci, if PARE data is provided then PARE-supported triggers are reported. It should be noted that the additional experimental data is optional and phastrigs can identify miRNA triggers with high accuracy even without such data.

Author:
Atul Kakrana
kakrana@udel.edu

Pingchuan Li
lipingchuan@gmail.com