Base Distribution

The base_distribution tool computes the average base composition at each position of the given region.

Note

This tool requires bedtools to be installed.

Usage

Usage:

PolTools base_distribution [-h] regions_file

Required Arguments

Description

Regions Filename

Bed formatted file containing all the regions you want to average the sequences. This file can be obtained by using the make_regions_file_centered_on_max_tss program

Behavior

base_distribution will report the position relative to the middle of the region and the percent occupancy of each base.

_images/base_distribution.png

For example:

$ head regions_centered_on_max_tss.bed
chr1    959251  959261  NOC2L   46      -
chr1    960627  960637  KLHL17  27      +
chr1    966516  966526  PLEKHN1 8       +
chr1    1000092 1000102 HES4    87      -
chr1    1000290 1000300 ISG15   12      +
chr1    1020114 1020124 AGRN    35      +
chr1    1074302 1074312 RNF223  10      -
chr1    1116102 1116112 C1orf159        9       -
chr1    1231967 1231977 SDF4    321     -
chr1    1232237 1232247 B3GALT6 174     +

$ PolTools base_distribution regions_centered_on_max_tss.bed
Position        A       T       G       C
-5.0    0.14846637102734664     0.1808019216555802      0.3518107908351811      0.3189209164818921
-4.0    0.15973762010347375     0.13470066518847007     0.2900960827790096      0.41546563192904656
-3.0    0.1271249076127125      0.17756836659275685     0.432649667405765       0.2626570583887657
-2.0    0.07843680709534367     0.23697339246119734     0.3852549889135255      0.29933481152993346
-1.0    0.021433850702143386    0.2683850702143385      0.0725240206947524      0.6376570583887657
1.0     0.5554323725055432      0.00803769401330377     0.35559866962305986     0.08093126385809313
2.0     0.16038433111603842     0.2354028085735403      0.3685328898743533      0.235679970436068
3.0     0.2156319290465632      0.2953621581670362      0.2557280118255728      0.2332779009608278
4.0     0.13848854397634885     0.27023281596452325     0.33379526977087953     0.25748337028824836
5.0     0.12601626016260162     0.23706577974870657     0.2983185513673319      0.33859940872135996