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Short | Long | Description
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–no-overlap | Ignore overlapping cis-regions
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–square | Output also the (signal) sum of square
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-i | –input | The input tiling dataset file (NMtdb)
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-o | –output | The stem name of the output file(s)
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-f | –feature | The feature file in gff format (version 3)
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-l | –feature-id | The file listing the feature types to focus on and/or directly the name of a feature type
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-u | –up-window | The window size (in bp) of the upstream region
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-d | –down-window | The window size (in bp) of the downstream region
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-p | –up-nclass | The number of bins into the upstream region will be split
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-w | –down-nclass | The number of bins into the downstream region will be split
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-s | –inside | The number of bins used to split the feature region
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-j | –col-from | The first column (from 0) from which threshold has to be computed
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-k | –col-to | The last column (from 0) from which threshold has to be computed
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