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2.29 NManout2 - Program Arguments

This program outputs the SNEPs together with additional information from results obtained by NManova2.

Short Long Description
–main-feature-only When –feature is used, output only parent features
–summary Output a single file with only the aligned nucleosomes and their statistics
-i –input The input directory
-o –output The output directory
-s –seqid The name of the chromosome to focus on
-f –feature A GFF (version 3) file providing the genomic annotations
-w –window The window (bp) around SNEP to look at
-p –pv-cutoff The p-value cut-off for calling SNEP
-m –prob-min The probability threshold above which aligned nuleosomes will be considered
-b –neighbour The number of nucleosomes to look at around each SNEP