#!/bin/bash
#use interactive session!
#module load Bowtie/1.2.2-foss-2018b

cd /data/kramseylab/compressed_fastq/230322_TnSeq/

echo -e "Mapping reads:\n" > 230404_mappinglog.txt

for f in *_trimmed.fastq;
do
    PREFIX1="${f%_trimmed.fastq}"

    bowtie --best -k 1 --fullref -v 0 -l 16 --threads 3 --sam /data/kramseylab/genomefiles/LVS_genome $PREFIX1\_trimmed.fastq > /data/kramseylab/sam/2304_TnSeq/$PREFIX1\.sam >> 230404_mappinglog.txt

    bowtie --best -k 1 --fullref -v 0 -l 16 --threads 3 --sam /data/kramseylab/genomefiles/LVS_genome Input_trimmed.fastq > /data/kramseylab/sam/2304_TnSeq/Input.sam
    bowtie --best -k 1 --fullref -v 0 -l 16 --threads 3 --sam /data/kramseylab/genomefiles/LVS_genome Day7_trimmed.fastq > /data/kramseylab/sam/2304_TnSeq/Day7.sam
    bowtie --best -k 1 --fullref -v 0 -l 16 --threads 3 --sam /data/kramseylab/genomefiles/LVS_genome Day14_trimmed.fastq > /data/kramseylab/sam/2304_TnSeq/Day14.sam

done