Mapping: Fungi - AndreaRP/METAGENOMICS GitHub Wiki

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Usage

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

bash mapper_fungi.sh [FUNGI_GENOME_REFERENCE] [HOST_FREE_READS_DIR]

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

bash wrapper_fungi_mapper.sh

Note: To run [wrapper_fungi_mapper.sh] (https://github.com/AndreaRP/METAGENOMICS/blob/wrapper/wrapper_fungi_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 fungi WG reference genome.
• 3. Creates fastq files using the BAM generated by bowtie2 which contains only reads that mapped the fungi WG reference.
• 4. Maps against fungi ITS reference genome.
• 5. Creates fastq files using the BAM generated by bowtie2 which contains only reads that mapped the fungi ITS reference.

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

##I/O

• Arguments:

  • $1 (fungiDB) = Directory of fungi reference genome (REFERENCES/FUNGI_GENOME_REFERENCE/)
  • $2 (sampleDir) = Directory to save output files. (ANALYSIS/05-fungi/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-fungi/sampleName/reads/)

  • sampleName_WG_fungi_R1.fastq: .fastq file with R1 reads that mapped the fungi WG DB.
  • sampleName_WG_fungi_R2.fastq: .fastq file with R2 reads that mapped the bacetria WG DB.
  • sampleName_WG_fungi_sorted.bam: sorted BAM file with the reads that mapped against the fungi Whole Genome reference.
  • sampleName_WG_fungi_sorted.bam.bai: index of the BAM file.
  • sampleName_WG_fungi_mapping.log: .log file with a log of the mapping of fungi WG DB.
  • (sampleName_WG_fungi_mapped.sam: SAM file from mapping the processed files against fungi Whole Genome reference. Intermediary file deleted on the run)
  • (sampleName_WG_fungi_mapped.bam: BAM file from mapping the processed files against fungi Whole Genome reference. Intermediary file deleted on the run)
  • sampleName_fungi_R1_ITS.fastq: .fastq file with R1 reads that mapped the fungi ITS DB.
  • sampleName_fungi_R2_ITS.fastq: .fastq file with R2 reads that mapped the bacetria ITS DB.
  • sampleName_fungi_sorted_ITS.bam: sorted BAM file with the reads that mapped against the fungi ITS reference.
  • sampleName_fungi_sorted.bam_ITS.bai: index of the BAM file.
  • sampleName_fungi_mapping_ITS.log: .log file with a log of the mapping of fungi ITS DB.
  • (sampleName_fungi_mapped_ITS.sam: SAM file from mapping the processed files against fungi ITS reference. Intermediary file deleted on the run)
  • (sampleName_fungi_mapped_ITS.bam: BAM file from mapping the processed files against fungi ITS reference. Intermediary file deleted on the run)