plot_virtual_4C

Concepts

plot_virtual_4C is used for visualizing chromatin interactions, similar to what the 4C (Circular Chromosome Conformation Capture) technique does. However, instead of performing a wet-lab 4C experiment, the tool uses processed data to virtually generate a 4C profile focused on interactions of a specific genomic region (viewpoint) with the rest of the genome.

One sample analysis

In this example, the sample range has been normalized using inherent normalization and the black triangle indicates our viewpoint chr1:40400000.

Interpreting the histogram

Changing the --width parameter

The bins used to create the histogram can be expanded by supplying a value with the --width parameter. The default --width value is 0.

Two-sample delta analyses

Changing the --height parameter

Usage

Usage and Option Summary

plot_virtual_4C
   -A H2K27ac \
   -G hg38 \
   -R chr1:40280000:40530000 \
   -V chr1:40400000

(or):

plot_virtual_4C
   -A H3K27ac \
   -B H3K27me3 \
   -G hg38 \
   -R chr1:40280000:40530000 \
   -V chr1:40400000

Required

| Short Option | Long Option | Description | |--------------|--------------|-------------| | -A | --sample1 | Name of the sample as it appears on the Tinkerbox | | -G | --genome | Genome build used for sample processing | | -R | --range | The genomic range to plot in chr:start:end format; -R chr1:40280000:40530000 | | -V | --viewpoint| The viewpoint to consider in chr:start format; -V chr1:40400000 |

Optional

| Short Option | Long Option | Description | |--------------|------------------|-------------| | -B | --sample2 | For two sample analyses, name of the second sample as it appears on the Tinkerbox | | | --sample1_dir | If not using the tinkerbox, specify the full path to the directory containing sample data | | | --sample2_dir | If not using the tinkerbox, full path to the second sample directory | | -Q | --norm | Which normalization to use: none, cpm, or aqua in lower case | | -r | --resolution | Resolution of sample in basepairs. Default 5000 | | -O | --output_name | Optional name for the plot | | | --quant_cut | Cap matrix values at a given percentile (0.00-1.00). Default 1.00 | | | --max_cap | Cap matrix values by adjusting the maximum value, modifies color intensity | | | --width | Number of bins up/downstream of viewpoint included in profile. Default 0 | | | --height | Value to control the height of the profile. Default calculated automatically | | -i | --inherent | If TRUE, normalize using inherent normalization. Default FALSE | | | --inh_col_floor | : Contact color for inherent values < 0, in RGB hexadecimal. Default FFFFFF | | | --inh_col_off | : Contact color for inherent values ~ 0, in RGB hexadecimal. Default D4E4FB | | | --inh_col_on | : Contact color for inherent values ~ 1, in RGB hexadecimal. Default FF0000 | | | --inh_col_ceil | : Contact color for inherent values > 1, in RGB hexadecimal. Default FF8D4A | | -h | --help | Help message |