Multicoverage

The multicoverage tool quantifies the number of 5’, 3’, or pileup reads in regions of sequencing files.

Note

This tool requires bedtools to be installed.

Usage

Usage:

PolTools multicoverage [-h] [-t [threads]]
                              read type regions_filename sequencing_files
                              [sequencing_files ...]

Required Arguments	Description
Read Type	Either five, three, or whole. Five and three will quantify the number of 5’ and 3’ end reads respectively. Whole will quantify the number of reads with any overlap in the regions.
Regions filename	Bed formatted file containing all the regions you want to quantify.
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

multicoverage will report the regions and the number of reads in each sequencing file in that region.

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 multicoverage five regions_centered_on_max_tss.bed seq_file.bed > output.tmp
$ head output.tmp
Chromosome      Left    Right   Name    Strand  seq_file.bed
chr1    959251  959261  NOC2L   -       73
chr1    960627  960637  KLHL17  +       59
chr1    966516  966526  PLEKHN1 +       12
chr1    1000092 1000102 HES4    -       146
chr1    1000290 1000300 ISG15   +       27
chr1    1020114 1020124 AGRN    +       44
chr1    1074302 1074312 RNF223  -       16
chr1    1116102 1116112 C1orf159        -       20
chr1    1231967 1231977 SDF4    -       531