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.
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