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2.15 NMhmmfit - Program Arguments

This program fits a Hidden Markov Model (HMM) to identify nucleosome along the genome based on the intensities of the tiling array.

Short Long Description
–full Fit the HMM on the entire chromosome, without sliding window
-i –input The input db file representing the tiling array dataset(s) (see NMtdb)
-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
-w –window The size of the sliding window (number of equally spaced probes)
-t –tiling The size of the tiling step (default is 4bp)
-m –iter-max The maximum number of iterations for the EM
-e –epsilon The convergence threshold for the EM
-s –wobs The minimal fraction of observed probes within a sliding window
-c –chrom The name of the chromosome to focus on