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Short | Long | Description
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–start | Look at the 5'end of the feature
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–end | Look at the 3'end of the feature
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–upstream | Look only at the upstream region of the feature boundary
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–matrix | Output the matrix of profiles
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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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-w | –window | The window size (in bp) around the each feature boundary
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-n | –nclass | The number of bins into which the upstream/downstream region will be split
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-c | –non-zero-col | Remove features for which the corresponding column in the dataset indicates no signal (see –zero-value)
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-z | –zero-value | The minimal value to consider the intensity as an actual signal to take into account
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