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te-nanopore-tools

A cache of scripts for manipulating nanopore/nanopolish output aimed at studying TEs

Plotting scripts

script description
composite_meth.py Plots multiple CpG methylation profiles against a reference TE, generally a consensus TE.
plotmeth_ref_hap.py Plots allele-specific CpG methylation profiles given a phased .bam, tabix-indexed nanopolish call-methylation output, and an interval of interest
plotmeth_ref_multi.py Plots one or more CpG metylation profiles given one or more phased .bams, each paired to a tabix-indexed nanopolish output, and an interval of interest
plotmeth_wg.py Plots the whole-genome methylation profile given output from wgmeth.py (see parsing tools)
segplot.py Makes strip plots or violin plots for specified samples given output from segmeth.py (see parsing tools)