Building chromatin traces
Contents
Building chromatin traces¶
Pre-processing¶
Two methods are used for pre-processing localization tables.
filter_localizations: removes localizations that do not achieve a user-defined threshold of intensity.register_localizations: applies local registration corrections to a localization table.
Building and processing trace tables¶
The main method for building chromatin traces is build_traces.
build_traces also supports optional BED-driven barcode/genomic annotation through the barcode_coordinates_BEDfile parameter in buildsPWDmatrix (see the detailed build_traces page below).
Chromatin trace tables can be post-processed using multiple scripts:
trace_analyser: quantifies several quantities from a trace table.trace_filter_advanced: applies advanced filtering to trace tables.trace_assign_mask: assigns a label to traces using a user-provided mask file.trace_combinator: combines/merges multiple trace tables (e.g. from different replicates or FOVs) using the folder architecture of pyHiM.trace_plot: script to plot one or multiple traces in 3D.
Building pairwise distance maps¶
Finally, trace tables can be converted to pairwise distance matrices using either the pyHiM built-in method:build_matrices, or using an external script: trace_to_matrix).