Posted update to 0.2.3 today, which fixes an error in the formatting of the BED files ... in all older versions the blockStarts field (column 12 of the bed line) was incorrectly reported in 1-based coordinates. With this fix, blockStarts are now correctly listed in zero-based coordinates per the BED specification.
Also note that I am working on a major new release, version 0.3.0, which will incorporate (at a minimum) the following new features:
1. The ability to provide a "flag-file" of coordinates corresponding to known elements of interest (e.g. repeats, mRNAs) or for flagging for exclusion (e.g. tRNAs, rRNAs, etc). The results file will flag small RNA clusters that overlap one or more of the loci in the flag-file. This will be useful for quality control, for instance in easily identifying clusters that are rRNA fragments or tRNA fragments, for instance.
2. Preset switches for animal vs. plant MIRNAs, which should enable bett
-- THIS WEBSITE HAS BEEN REPLACED ... please go to http://sites.psu.edu/axtell for the current Axtell Lab Website! --
Michael Axtell, lab PI