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2.13 NMt2featcis - Program Arguments

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