Metaplot

The metaplot tool computes the average coverage of [5’/3’/pileup] reads of sequencing data around the center of features provided.

Note

This tool requires bedtools to be installed.

Usage and option summary

Usage:

PolTools metaplot [-h] [-t [threads]]
                         read type regions_file sequencing_files
                         [sequencing_files ...]

Required Arguments	Description
Read type	Either five, three or whole corresponding to 5’ ends, 3’ ends, or pileup reads.
Regions File	Bed formatted file containing all the regions to quantify (+1 nucleotide centered). These regions can be made 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

metaplot will report the position relative to the center of the regions provided and the average of the [5’, 3’, or pileup] reads at that position.

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     +

$ 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     -

$ PolTools three CCNT1_inr.bed control.bed
Position       seq_file.bed 3' sense strand    seq_file.bed 3' divergent strand
-5.0    0.8859940872135994      -0.01579822616407982
-4.0    0.6057834441980784      -0.013673318551367332
-3.0    0.7096267553584626      -0.008961566888396156
-2.0    1.2311529933481153      -0.013673318551367332
-1.0    0.5052660753880266      -0.02836289726533629
1.0     1.432280118255728       -0.00655949741315595
2.0     0.7416851441241685      -0.01607538802660754
3.0     0.7222838137472284      -0.012564671101256468
4.0     1.445861049519586       -0.010809312638580931
5.0     1.1093865484109386      -0.014689578713968959