TPS Distance Per Gene

The tps_distance_per_gene tool computes the most commonly used transcript length for each region in the region file centered on the max TSS.

Note

This tool requires bedtools to be installed.

Usage

Usage:

PolTools tps_distance_per_gene [-h] [-t [threads]]
                                      regions_filename sequencing_files
                                      [sequencing_files ...]

Required Arguments	Description
Regions filename	Bed formatted file containing all the regions you want to quantify (must be centered on +1 nt). This file can be generated from the make_regions_file_centered_on_max_tss program
Sequencing Files	Bed formatted file from a sequencing experiment.

Optional Arguments	Description
-t, –threads	Maximum number of threads. Default is the number of threads on the system. This program will not use more threads than the number of sequencing files provided
Sequencing Files	Additional sequencing files can be provided.

Behavior

tps_distance_per_gene will report the most commonly used transcript length from the maxTSS (regions file centered) for each gene

For example:

$ head seq_file.bed
chr1    11981   12023   A00876:119:HW5F5DRXX:1:2168:2248:1407   255     -
chr1    13099   13117   A00876:119:HW5F5DRXX:1:2203:31403:26757 255     -
chr1    13356   13423   A00876:119:HW5F5DRXX:1:2151:15808:7827  255     -
chr1    13435   13477   A00876:119:HW5F5DRXX:1:2273:15781:19241 255     -
chr1    13739   13772   A00876:119:HW5F5DRXX:1:2256:29966:10520 255     -
chr1    13741   13773   A00876:119:HW5F5DRXX:1:2235:4101:11882  255     -
chr1    14178   14203   A00876:119:HW5F5DRXX:1:2115:8241:31422  255     -
chr1    14734   14768   A00876:119:HW5F5DRXX:1:2165:23764:2440  255     -
chr1    14988   15012   A00876:119:HW5F5DRXX:1:2219:16134:32784 255     -
chr1    18337   18362   A00876:119:HW5F5DRXX:1:2149:32054:31328 255     -

$ 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 tps_distance_per_gene regions_centered_on_max_tss.bed seq_file.bed > seq_file_tps_distance_per_gene.txt
$ head seq_file_tps_distance_per_gene.txt
Gene    seq_file.bed
NOC2L   32
KLHL17  42
PLEKHN1 45
HES4    16
ISG15   44
AGRN    33
RNF223  35
C1orf159        N/A
SDF4    68