Mapping: Parasite - AndreaRP/METAGENOMICS GitHub Wiki

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Usage

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

bash mapper_parasite.sh [REFERENCES_DIR] [HOST_FREE_READS_DIR]

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

bash wrapper_parasite_mapper.sh

Note: To run [wrapper_parasite_mapper.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_parasite_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 protozoa reference genome.
• 3. Generates fastq files using the bam generated by bowtie2 which contains only reads that mapped the protozoa reference.
• 4. Maps against invertebrate reference genome.
• 5. Generates fastq files using the bam generated by bowtie2 which contains only reads that mapped the reference.

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

##I/O

• Arguments:

  • $1 (DB) = Directory of parasite reference genome (REFERENCES/)
  • $2 (sampleDir) = Directory containing noHost 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.

• Protozoa output files: (In ANALYSIS/08-protozoa/sampleName/reads/)

  • sampleName_protozoa_R1.fastq: .fastq file with R1 reads that mapped the protozoa protozoa DB.
  • sampleName_protozoa_R2.fastq: .fastq file with R2 reads that mapped the protozoa protozoa DB.
  • sampleName_protozoa_sorted.bam: sorted BAM file with the reads that mapped against the protozoa Whole Genome reference.
  • sampleName_protozoa_sorted.bam.bai: index of the BAM file.
  • sampleName_protozoa_mapping.log: .log file with a log of the mapping of protozoa DB.
  • (sampleName_protozoa_mapped.sam: SAM file from mapping the processed files against protozoa Whole Genome reference. Intermediary file deleted on the run)
  • (sampleName_protozoa_mapped.bam: BAM file from mapping the processed files against protozoa Whole Genome reference. Intermediary file deleted on the run)

• Invertebrate output files: (In ANALYSIS/09-invertebrate/sampleName/reads/)

  • sampleName_invertebrate_R1.fastq: .fastq file with R1 reads that mapped the invertebrate invertebrate DB.
  • sampleName_invertebrate_R2.fastq: .fastq file with R2 reads that mapped the invertebrate invertebrate DB.
  • sampleName_invertebrate_sorted.bam: sorted BAM file with the reads that mapped against the invertebrate Whole Genome reference.
  • sampleName_invertebrate_sorted.bam.bai: index of the BAM file.
  • sampleName_invertebrate_mapping.log: .log file with a log of the mapping of invertebrate DB.
  • (sampleName_invertebrate_mapped.sam: SAM file from mapping the processed files against invertebrate Whole Genome reference. Intermediary file deleted on the run)
  • (sampleName_invertebrate_mapped.bam: BAM file from mapping the processed files against invertebrate Whole Genome reference. Intermediary file deleted on the run)