hisat2_ref.sh

#!/bin/bash

# Check if exactly three arguments are provided
if [ $# -ne 3 ]; then
    echo "Usage: $0 <reference_genome.fna> <annotation.gtf> <reads.fastq>"
    exit 1
fi

HISAT2_PATH="/home/xren15/mambaforge/bin/hisat2"

REF_GENOME=$1
ANNOTATION=$2
READS=$3
SPLICE="$(dirname "$ANNOTATION")/splice.ss"
EXON="$(dirname "$ANNOTATION")/exon.exon"
REF_PREFIX="$(dirname "$REF_GENOME")/$(basename "$REF_GENOME" .fna)"
READS_FILENAME=$(basename "$READS" | cut -f1 -d'.')

python3 hisat2-2.2.1/hisat2_extract_exons.py $ANNOTATION > $SPLICE
python3 hisat2-2.2.1/hisat2_extract_splice_sites.py $ANNOTATION > $EXON

<<<<<<< HEAD
# WORKING_DIR="/data/mschatz1/xren15/hisat2"
# mkdir -p $WORKING_DIR
$HISAT2_PATH-build --ss hisat2-2.2.1/hisat2_extract_exons.py --exon hisat2-2.2.1/hisat2_extract_splice_sites.py $REF_GENOME $REF_PREFIX
=======
WORKING_DIR="/data/mschatz1/xren15/hisat2"
mkdir -p $WORKING_DIR
$HISAT2_PATH-build --tmp $WORKING_DIR --ss hisat2-2.2.1/hisat2_extract_exons.py --exon hisat2-2.2.1/hisat2_extract_splice_sites.py $REF_GENOME $REF_PREFIX
>>>>>>> bea5162 (updated hisat2 script)

OUTPUT_SAM="hisat2/${READS_FILENAME}/aligned_reads.sam"
ALIGNMENT_SUMMARY="hisat2/${READS_FILENAME}/alignment_summary.txt"

mkdir -p "hisat2/${READS_FILENAME}"
{ time $HISAT2_PATH -x $REF_PREFIX -U $READS -S $OUPUT_SAM ; } > $ALIGNMENT_SUMMARY 2>&1