scripts/mahendrawada_orig_scripts/ALIGNMENT_BOWTIE2.sh

#!/bin/bash

# Load Bowtie2 module for alignment
module load Bowtie2

# Read project name from a file and set up output log path
project=$(cat ../project.txt)
output=~/ngs/$project/summary/bowtie2.log

# Log the start time and Bowtie2 version
echo "Processing fastq files on" $(date) > $output
printf "\n" >> $output
bowtie2 --version >> $output
printf "\n" >> $output

# Define paths to reference genomes for alignment
cerevisiae=/shared/biodata/ngs/Reference/iGenomes/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/genome
drosophila=/shared/biodata/ngs/Reference/iGenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/genome

# Define input and output directories
fastq_dir=/home/ngs/fast/fastq/$project/
sam_dir=/home/ngs/fast/sam/$project/

# Loop through each sample name listed in the sample_names.txt file
for i in $(cat ../sample_names.txt); do
  echo "Results for sample:" $i >> $output

  # Create a list of all R1 fastq files for the current sample
  ls ${fastq_dir}*${i}*R1*fastq > ${i}_fastq_R1.list
  count=0

  # Loop through each R1 fastq file and perform paired-end alignment
  for j in $(cat ${i}_fastq_R1.list); do
    # Identify corresponding R2 fastq file by replacing '_R1' with '_R2'
    k=$(echo $j | sed 's/_R1/_R2/')

    # Run Bowtie2 alignment for the first read pair, including headers
    if [ $count -lt 1 ]; then
      # Align against Saccharomyces cerevisiae genome
      bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700 --threads 12 -x $cerevisiae -1 $j -2 $k > ${sam_dir}/${i}.sam 2>> $output
      
      # Align against Drosophila melanogaster genome
      bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700 --threads 12 -x $drosophila -1 $j -2 $k > ${sam_dir}/${i}_dm.sam 2>> $output
    else
      # Subsequent alignments for the same sample (without headers)
      bowtie2 --no-head --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700 --threads 12 -x $cerevisiae -1 $j -2 $k >> ${sam_dir}/${i}.sam 2>> $output
      
      # Subsequent alignments against Drosophila genome
      bowtie2 --no-head --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700 --threads 12 -x $drosophila -1 $j -2 $k >> ${sam_dir}/${i}_dm.sam 2>> $output
    fi

    # Increment count for managing header inclusion
    count=$(echo "print($count + 1)" | python3)
  done

  # Add spacing in the output log after processing each sample
  printf "\n" >> $output

  # Clean up temporary file listing R1 fastq files
  rm ${i}_fastq_R1.list
done