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This program outputs the SNEPs together with additional information from results obtained by NManova2.
Short | Long | Description
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–main-feature-only | When –feature is used, output only parent features
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–summary | Output a single file with only the aligned nucleosomes and their statistics
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-i | –input | The input directory
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-o | –output | The output directory
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-s | –seqid | The name of the chromosome to focus on
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-f | –feature | A GFF (version 3) file providing the genomic annotations
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-w | –window | The window (bp) around SNEP to look at
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-p | –pv-cutoff | The p-value cut-off for calling SNEP
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-m | –prob-min | The probability threshold above which aligned nuleosomes will be considered
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-b | –neighbour | The number of nucleosomes to look at around each SNEP
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