Plot_coverage-Sit

This bash script calculates the coverage depth in a desired window, and then calling the R script it outputs a plot with the depth coverage on each chromosome.

FILES

• Depth.sh = Bash script for launching the depth analysis of a bam file, creating the corresponding bed for a window lenght and plotting the coverage accross the chromosomes with an Rscript included in the folder.

• Coverage_in_windows_singlepage.R = Rscript for creating the plot from a bed file and a window length.

First step

Download the zip directory and decompress it, or clone this repository in your computer. Then move to the directory. In order to be able to run correctly the Depth.sh script you'll have to modify one of the first lines of it:

export PATH:$PATH="path/of/R/script/"

And specify the correct path to the directory where you have te Rscript stored in your computer.

Usage

To do the depth analysis you have to call the bash script from the terminal the following way:

sbatch depth.sh <window_width> <file.bam> <desired/output/path>

The 3 arguments you have to provide are mandatory, if you use less than 3 arguments the program will break. Those arguments correspond to:

• <window_width>: Enter a value of the desired window width for calculating the depth coverage.
• <file.bam>: Specify the input BAM file, enter the whole path.
• <output/desired/path/>: Specify the desired path where you want to save the output files.

This is an example of the usage of this script:

sbatch depth.sh 100 /users/Desktop/bams/h_sap_2039.bam /users/Desktop/bams/results/

Output

On your specified output directory you'll find several files. First, there are the ones from the depth calculation with the mosdepth software. The most important is the one ending with regions.bed.gz. This file contains de coverage depth calculation for the specified window, and is the one used to do the plot.

Then you'll have a pdf file names as the basename of the bam file used as input and ending with _window.pdf where window stands for the value of the specified window length for the depth coverage calculation. In here you'll have a visual representation of the distribution of the coverage along each chromosome.