Coverage_Mapping

Basic Usage

The Coverage_Map.sh script generates text-based histograms, or maps, from BEDTools' coverage tool. This script accepts a list of BAM files as its input and will generate a coverage map for each BAM file specified. This script will not plot the coverage maps, it will only generate them. To run Coverage_Map.sh, all variables must be defined within the file itself. This is accomplished by opening Coverage_Map.sh in your favorite text editor and following instructions in the usage information section. Once the variables have been defined, Coverage_Map.sh needs to be submitted to a job scheduler. The script is set up for PBS and submitting Coverage_Map.sh is done with the following command:

qsub Coverage_Map.sh

After the job has run, a list of coverage maps will be generated, please view the output file from the job submission to obtain the path to the list.

Variables

The following are a list of variables that need to be defined within Coverage_Map.sh, read the output file generated from the job submission to get the path to the list.

Variable	Line	Function
Email	5	Sets an email address for notifications of job status
BEDTools Definition	46-48	Define the path to the SAMTools installation or load it from a cluster
SAMPLE_INFO	41	A list of BAM files to map
PROJECT	54	A name that describes the project you are working on
SCRATCH	57	A directory that will hold results
REF_ANN	51	A reference annotation, either BED or GFF format, used in the mapping process

Output

Coverage_Map.sh generates coverage maps for each BAM file specified. In addition, a list of all coverage maps is created for use in other scripts.

Dependencies

Coverage_Map.sh depends on BEDTools for generating the coverage maps. In addition, PBS and GNU Parallel are required for basic running.

Next: Plot_Coverage.sh