I am pleased to present a new tool for analysis of small RNA sequencing data -- ShortStack. This program is designed for comprehensive annotation of small RNA-producing genes, including siRNA clusters, phased small RNAs, hairpin-derived small RNAs, and MIRNAs. Loci are discovered de novo and annotated with the statistics that are relevant for small RNAs .. size, polarity, repetitiveness, phasing, and underlying hairpins. In addition, ShortStack can be run in 'count' mode to quantify and annotate a set of loci provided a priori by the user. If you have smallRNA-seq data (and a reference genome to align it to), give the beta ShortStack version a try (and give me your comments at firstname.lastname@example.org).
-- THIS WEBSITE HAS BEEN REPLACED ... please go to http://sites.psu.edu/axtell for the current Axtell Lab Website! --
Michael Axtell, lab PI