Mapping: Virus

Graph

Usage

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

bash mapper_virus.sh [VIRUS_GENOME_REFERENCE] [HOST_FREE_READS_DIR]

Multiple samples: [wrapper_virus_mapper.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_virus_mapper.sh)

bash wrapper_virus_mapper.sh

Note: To run [wrapper_virus_mapper.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_virus_mapper.sh) you must have generated the sample name list with Sample Name list generator

In a nutshell...

• 1. Creates necessary directories.
• 2. Maps against virus reference genome.
• 3. Generates fastq files using the bam generated by bowtie2 which contains only reads that mapped the virus reference.

Note: This script should be run after filtering the host.

##I/O

• Arguments:

  • $1 (virDB) = Directory of parasite reference genome (REFERENCES/VIRUS_GENOME_REFERENCE/).
  • $2 (sampleDir) = Directory containing host-free files. (ANALYSIS/04-noHost/sampleName/)

• Input Files: (In ANALYSIS/04-noHost/sampleName/)

  • sampleName_noHost_R1.fastq: fastq file with the R1 reads of the sample after filtering the host.
  • sampleName_noHost_R2.fastq: fastq file with the R2 reads of the sample after filtering the host.

• Output files: (In ANALYSIS/06-virus/sampleName/reads/)

  • sampleName_virus_R1.fastq: .fastq file with R1 reads that mapped the virus virus DB.
  • sampleName_virus_R2.fastq: .fastq file with R2 reads that mapped the bacetria virus DB.
  • sampleName_virus_sorted.bam: sorted BAM file with the reads that mapped against the virus Whole Genome reference.
  • sampleName_virus_sorted.bam.bai: index of the BAM file.
  • sampleName_virus_mapping.log: .log file with a log of the mapping of virus virus DB.
  • (sampleName_virus_mapped.sam: SAM file from mapping the processed files against virus Whole Genome reference. Intermediary file deleted on the run)
  • (sampleName_virus_mapped.bam: BAM file from mapping the processed files against virus Whole Genome reference. Intermediary file deleted on the run)