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This program aligns the nucleosome occupancy profiles from a query genome onto a reference genome. It is much more faster than NMalign.
Short | Long | Description
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Print in text format the alignments
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-i | –input | The input directory containing alignment files (with –print)
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-c | –config | The input configuration file
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-o | –output | The output directory
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-s | –chrom | The name of the chromosome to focus on
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-t | –tiling | The size of the tiling step (default is 4bp)
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-m | –nucmin | The minimal number of probes covering a nucleosome
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-v | –ovrmin | The minimal number of probes covering a nucleosome
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-g | –coverage | The coverage fraction w.r.t to the average size of the nucleosome
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