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