Our paper is finally out!
A group of very talented students and staff at Hanah Margalit's lab here in Jerusalem were busy developing a new and exciting experimental method for mapping small RNA - mRNA interactions in bacteria. The method includes IP of the chaperon Hfq protein, ligation of RNAs and paired-end sequencing resulting in chimeric fragments (usually sRNA-mRNA). The package RILseq (https://pypi.python.org/pypi/RILseq and https://github.com/asafpr/RILseq) accompanies this experimental procedure and provides all the steps, from mapping the reads to statistical inference of true interactions.
The paper: http://www.cell.com/molecular-cell/fulltext/S1097-2765(16)30413-0
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May I suggest going with the modern text UI interface - where instead of lenghty and complicated script names such as
RILseq_significant_regions.pythe tool provides a simpler interface that allows self discovery in the mannerbwaandbedtoolsdo.It is nearly impossible to remember the script name above whereas if the tool was simply called
rilwould allow users to interactively discover all usage scenarios and would work via a simpler constructs such as:That's a great advice, I guess we can wrap it as you suggested. Thank you very much for the input!