-This repository contains all scripts and commands to obtain statistics of mapped metagenomic reads to reference genomes.
*Dependencies
Samtools 1.5 or higher https://github.com/samtools/samtools
Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Bedtools https://bedtools.readthedocs.io/en/latest/
Prodigal https://github.com/hyattpd/Prodigal
The main script Mapping_and_RPKM.total.sh runs Bowtie2 for indexing and mapping metagenomic reads to a reference genome. It produces all sorted and indexed BAM files for basic Stats calculations with Samtools stats command. Additionally, gff and CDS files are predicted with Prodigal. It uses CDS and gff for RPKM (RPKM.R) calculation obtaining the counts (mapped reads) for each CDS with multicov from Bedtools, at the end multple statistics from CDS and RPKM values are retrieved (STATS.RPKM.R).
For running in a directory with fasta files from Refence genome and metagenomic reads (paired) from metagenomes type:
./Mapping_and_RPKM.total.sh <Genomes_suffix_fasta_files> <Metagenome_Read_1.fq> <Metagenome_Read_2.fq> <cpu> <path_to_Metagenomic_scripts>