v1.1.0

October 1, 2013.

Version 1.1.0 release notes:
Multiple small RNA-seq datasets can now be input into a single run, to create a single merged alignment file with each read's origin tracked by read group.
New option --read_group allows the user to specify analysis to be performed using only data from a single read group (when using a bam alignment file comprised of alignments from multiple read groups).
Upon completion of analysis of an alignment containing more than one read-group, ShortStack will now by default automatically perform --count mode analysis of EACH read group separately. This facilitates gathering count data to be used for downstream differential expression analyses.
Tutorial data and procedures updated at http://axtelldata.bio.psu.edu/data/ShortStack_TestData/.