Mapping: Bacteria - AndreaRP/METAGENOMICS GitHub Wiki

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

bash mapper_bacteria.sh [BACTERIA_GENOME_REFERENCE] [HOST_FREE_READS_DIR]

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

bash wrapper_bacteria_mapper.sh

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

In a nutshell...

    1. Creates necessary directories.
    1. Maps against bacteria WG reference genome.
    1. Creates fastq files using the bam generated by bowtie2 which contains only reads that mapped the bacteria WG reference.
    1. Maps against bacteria 16S reference genome.
    1. Creates fastq files using the bam generated by bowtie2 which contains only reads that mapped the bacteria 16S reference.

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

##I/O

  • Arguments:

    • $1 (bacDB) = Directory of bacteria reference genome (REFERENCES/BACTERIA_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/05-bacteria/sampleName/reads/)

    • sampleName_WG_bacteria_R1.fastq: .fastq file with R1 reads that mapped the bacteria WG DB.
    • sampleName_WG_bacteria_R2.fastq: .fastq file with R2 reads that mapped the bacetria WG DB.
    • sampleName_WG_bacteria_sorted.bam: sorted BAM file with the reads that mapped against the bacteria Whole Genome reference.
    • sampleName_WG_bacteria_sorted.bam.bai: index of the BAM file.
    • sampleName_WG_bacteria_mapping.log: .log file with a log of the mapping of bacteria WG DB.
    • (sampleName_WG_bacteria_mapped.sam: SAM file from mapping the processed files against bacteria Whole Genome reference. Intermediary file deleted on the run)
    • (sampleName_WG_bacteria_mapped.bam: BAM file from mapping the processed files against bacteria Whole Genome reference. Intermediary file deleted on the run)
    • sampleName_bacteria_R1_16S.fastq: .fastq file with R1 reads that mapped the bacteria 16S DB.
    • sampleName_bacteria_R2_16S.fastq: .fastq file with R2 reads that mapped the bacetria 16S DB.
    • sampleName_bacteria_sorted_16S.bam: sorted BAM file with the reads that mapped against the bacteria 16S reference.
    • sampleName_bacteria_sorted.bam_16S.bai: index of the BAM file.
    • sampleName_bacteria_mapping_16S.log: .log file with a log of the mapping of bacteria 16S DB.
    • (sampleName_bacteria_mapped_16S.sam: SAM file from mapping the processed files against bacteria 16S reference. Intermediary file deleted on the run)
    • (sampleName_bacteria_mapped_16S.bam: BAM file from mapping the processed files against bacteria 16S reference. Intermediary file deleted on the run)