Next: , Previous: NMhmmvit - Examples, Up: Programs


2.19 NMalign - Program Arguments

This program aligns the nucleosome occupancy profiles from a query genome onto a reference genome.

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
-k –prb-mapped The minimal fraction of nucleosomal probes that can be mapped on both the ref and the qry (default is 1.0), otherwise nucleosome is discarded
-l –prb-overlap The minimal overlap between the reference and query nucleosomes to be considered as aligned (default is 0.85)