Coverage_Mapping

Basic Usage

The Coverage_Mapping handler 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. To run Coverage_Mapping, all common variables and handler-specific variables must be defined within the configuration file. Once the variables have been defined, Coverage_Mapping can be submitted to a job scheduler with the following command:

sequence_handling Coverage_Mapping Config

Where Config is the full file path to the configuration file.

Handler-Specific Variables

The following are a list of variables that need to be defined within Config. In addition to the handler-specific variables, all common variables must be defined.

Variable	Function
CM_QSUB	QSub settings for batch submission. Recommended settings are "mem=12gb,nodes=1:ppn=8,walltime=24:00:00".
REF_ANN	A reference annotation, either BED or GFF format, used in the mapping process.

Output

Coverage_Mapping generates coverage maps for each BAM file specified. The plots will be generated in pdf format and located at

${OUT_DIR}/Coverage_Mapping/CoveragePlots/${SAMPLE}_plot.pdf

Dependencies

Coverage_Mapping depends on BEDTools and R for generating the coverage maps. In addition, PBS and GNU Parallel are required for basic operation.