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This program
Short | Long | Description
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–sliding | Use a sliding window instead of contiguous bins
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-i | –input | The input directory
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-d | –data | The data file
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-o | –output | The output file
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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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-l | –feature-id | A file listing the features to consider
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