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This program aligns the nucleosome occupancy profiles from a query genome onto a reference genome.
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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-k | –prb-mapped | The minimal fraction of nucleosomal probes that can be mapped on both the ref and the qry (default is 1.0), otherwise nucleosome is discarded
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-l | –prb-overlap | The minimal overlap between the reference and query nucleosomes to be considered as aligned (default is 0.85)
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