STAR--比对

#!/bin/bash
###########################################################
#SBATCH -t 2380:00:00
#SBATCH -N 1
#SBATCH --cpus-per-task=20
#SBATCH -p cv2
#SBATCH -o job.out
#SBATCH -e job.err
cd $SLURM_SUBMIT_DIR

# Define the path to the STAR executable

# Define the path to the reference genome index
genomeDir="/public/home/jiezhang_gibh/hqn1/rnaseq1014/fastqnew.data/trim/h19/index"

# Define the output directory
outputDir="/public/home/jiezhang_gibh/hqn1/rnaseq1014/fastqnew.data/trim/star"

# Loop through each pair of sequencing data files
for i in BHLHE40-rep1 BHLHE40-rep2 Control-rep1 Control-rep2
do
        read1="/public/home/jiezhang_gibh/hqn1/rnaseq1014/fastqnew.data/trim/${i}_1_val_1.fq.gz"
        read2="/public/home/jiezhang_gibh/hqn1/rnaseq1014/fastqnew.data/trim/${i}_2_val_2.fq.gz"
        gzip -d $read1
        gzip -d $read2
        R1="/public/home/jiezhang_gibh/hqn1/rnaseq1014/fastqnew.data/trim/${i}_1_val_1.fq"
        R2="/public/home/jiezhang_gibh/hqn1/rnaseq1014/fastqnew.data/trim/${i}_2_val_2.fq"
# Run STAR alignment
        STAR --runThreadN 20 --genomeDir $genomeDir --readFilesIn $R1 $R2 --outFileNamePrefix ${outputDir}/${i} --outSAMtype BAM SortedByCoordinate
done