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2.17 NMhmmvit - Program Arguments

This program performs the Viterbi algorithm on the results of NMhmmfit to call the nucleosomes.

Short Long Description
–rm-outlier Remove probes with obvious spurious estimates
–print Print in text format the output of NMhmmfit
-i –input The input db file representing the tiling array dataset(s) (see NMtdb)
-r –result The directory containing the files generated by NMhmmfit
-o –output The output directory
-x –nmax The maximum number of probes for a well-localized nucleosome
-n –nmin The minimum number of probes for a well-localized nucleosome
-t –tiling The size of the tiling step (default is 4bp)
-l –chunk-min The minimal size of probe chunks to be included
-m –remove-min
-c –chrom The name of the chromosome to focus on