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2.21 NMalign2 - Program Arguments

This program aligns the nucleosome occupancy profiles from a query genome onto a reference genome. It is much more faster than NMalign.

Short Long Description
–print Print in text format the alignments
-i –input The input directory containing alignment files (with –print)
-c –config The input configuration file
-o –output The output directory
-s –chrom The name of the chromosome to focus on
-t –tiling The size of the tiling step (default is 4bp)
-m –nucmin The minimal number of probes covering a nucleosome
-v –ovrmin The minimal number of probes covering a nucleosome
-g –coverage The coverage fraction w.r.t to the average size of the nucleosome