5-RACE/run_alignment.sh at main · Boyle-Lab/5-RACE · GitHub

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#!/bin/bash
cat <<EOF
#!/bin/bash
#SBATCH --job-name=${1}.${2}.${3}.run_alignment
#SBATCH --cpus-per-task=1
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem-per-cpu=20g
#SBATCH --time=5:00:00
#SBATCH --account=
#SBATCH --partition=
#SBATCH --output=logs/%x.log

module load Bioinformatics
module load minimap2/2.14-jvscyil
module load samtools

REF_FA="/path/to/hg38_no_alt.mmi"
SPLICE_FA="/path/to/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
DATA_DIR=""

EXP="$1"
SAMPLE="$2"
PRIMER="$3"

SAMPLE_FASTQ="\${DATA_DIR}/\${EXP}/\${SAMPLE}_\${PRIMER}.fastq.gz"
SAMPLE_SAM="\${DATA_DIR}/\${EXP}/\${SAMPLE}_\${PRIMER}.sam"
SPLICE_SAM="\${DATA_DIR}/\${EXP}/\${SAMPLE}_\${PRIMER}.splice.sam"

SORTED_BAM="\${DATA_DIR}/\${EXP}/\${SAMPLE}_\${PRIMER}.sorted.bam"
SORTED_BAI="\${DATA_DIR}/\${EXP}/\${SAMPLE}_\${PRIMER}.sorted.bai"

SPLICE_BAM="\${DATA_DIR}/\${EXP}/\${SAMPLE}_\${PRIMER}.splice.sorted.bam"
SPLICE_BAI="\${DATA_DIR}/\${EXP}/\${SAMPLE}_\${PRIMER}.splice.sorted.bai"

minimap2 -ax map-ont --secondary=no \${REF_FA} \${SAMPLE_FASTQ} > \${SAMPLE_SAM}
samtools sort \${SAMPLE_SAM} | samtools view -bS > \${SORTED_BAM}
samtools index \${SORTED_BAM}
rm \${SAMPLE_SAM}

minimap2 -ax splice --secondary=no \${SPLICE_FA} \${SAMPLE_FASTQ} > \${SPLICE_SAM}
samtools sort \${SPLICE_SAM} | samtools view -bS > \${SPLICE_BAM}
samtools index \${SPLICE_BAM}
rm \${SPLICE_SAM}

exit
EOF