Mapping-Kallisto

#!/bin/bash

#SBATCH -p compute
#SBATCH --output=rnaSPADES%a.out
#SBATCH -t 4-0
#SBATCH --mem=500G
#SBATCH -c 64
#SBATCH --array=0-0

# load modules
module load bioinfo-ugrp-modules DebianMed/12.0
module load kallisto/0.48.0+dfsg-3

# Path
trimmed_reads="/path/to/trimmed/reads"
reference="/path/to/ref"
output="/path/to/kallisto/output"

# Create arrays of forward and reverse reads
reads1=(${trimmed_reads}/*_L001_R1_trimmed.fastq.gz) # forward reads
reads2=(${trimmed_reads}/*_L001_R2_trimmed.fastq.gz) # reverse reads

# Access individual read pairs using SLURM array index
fwd_read=${reads1[$SLURM_ARRAY_TASK_ID]}
rev_read=${reads2[$SLURM_ARRAY_TASK_ID]}

# Output directory names
name=$(basename "$fwd_read" _R1_trimmed.fastq.gz)

#Create an index from your reference transcriptome
kallisto index --make-unique -i ${reference}/transcripts.idx ${reference}/transcripts.fasta

#Map the reads to the reference transcriptome index
kallisto quant -i ${reference}/transcripts.idx -o $output $fwd_read $rev_read