Coverage

Graph

Usage

Single sample: [coverage.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/coverage.sh)

bash coverage.sh [SAMPLE_ORGANISM_DIR] [ORGANISM_REFERENCE_DIR]

Multiple samples:

Bacteria: [wrapper_bacteria_coverage.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_bacteria_coverage.sh)

bash wrapper_bacteria_coverage.sh

Virus: [wrapper_virus_coverage.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_virus_coverage.sh)

bash wrapper_virus_coverage.sh

Fungi: [wrapper_fungi_coverage.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_fungi_coverage.sh)

bash wrapper_fungi_coverage.sh

Parasite: [wrapper_parasite_coverage.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_parasite_coverage.sh)

bash wrapper_parasite_coverage.sh

Note: To run any of wrapper scripts above you must have generated the sample name list with Sample Name list generator.

In a nutshell...

• 1. Creates necessary directories.
• 2. Calculates coverage using [bedtools] (http://bedtools.readthedocs.io/en/latest/).
• 3. Creates coverage files and graphs using an [R script] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/graphs_coverage.R).

Note: This script can only be run after mapping.

##I/O

• Arguments:

  • $1 = (sampleDir) Directory where the analysis is. (ANALYSIS/xx-organism/sampleName/)
  • $2 = (refDB) Directory with the references. (/REFERENCES/ORGANISM_GENOME_REFERENCE)

• Input Files:

  • genomeLength: List of the length of each of the genomes in the reference DB- (REFERENCES/ORGANISM_GENOME_REFERENCE/WG/genome_length.txt)
  • sampleBam: BAM file of the sample generated after mapping. (ANALYSIS/xx-organism/sampleName/reads/)

• Output files:(In ANALYSIS/xx-organism/sampleName/coverage)

  • sampleName_genome_coverage.txt: Coverage file from the BAM file.
  • sampleName_coverage_log.log: Log file.