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This program performs the Viterbi algorithm on the results of NMhmmfit to call the nucleosomes.
Short | Long | Description
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–rm-outlier | Remove probes with obvious spurious estimates
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Print in text format the output of NMhmmfit
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-i | –input | The input db file representing the tiling array dataset(s) (see NMtdb)
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-r | –result | The directory containing the files generated by NMhmmfit
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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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-t | –tiling | The size of the tiling step (default is 4bp)
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-l | –chunk-min | The minimal size of probe chunks to be included
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-m | –remove-min |
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-c | –chrom | The name of the chromosome to focus on
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