align_single_test.sh

#!/bin/bash


#$ -cwd
#$ -l h_vmem=40G
#$ -e error
#$ -o output

echo "Loading modules..."
source /etc/profile.d/modules.sh
module load igmm/apps/STAR/2.7.8a
module load igmm/apps/cutadapt/1.16

echo "Copying sequence files to current dir..."
cp $SEQUENCE_PATH/B001/2*.gz .

echo "running cutadapt_single.py from code folder..."
python3 ~/Code/RNAseq/linear/cutadapt_single.py

echo "unzipping output..."
gunzip trimmed*.gz

echo "Cleaning up compressed files..."
rm *.gz

unique_part=$(for file in *.fastq; do echo $file | cut -f1 -d "." | cut -f7 -d "_";  done | uniq)

# Concatenate the R1 and R2 files from different lanes
echo "Concatenating files..."
cat trimmed_220721_A00291_0453_AH7JGYDRX2_*_${unique_part}_1.fastq > trimmed_merged_220721_A00291_0453_AH7JGYDRX2_${unique_part}_1.fastq
cat trimmed_220721_A00291_0453_AH7JGYDRX2_*_${unique_part}_2.fastq > trimmed_merged_220721_A00291_0453_AH7JGYDRX2_${unique_part}_2.fastq
rm trimmed_220721_A00291_0453_AH7JGYDRX2_*_${unique_part}_1.fastq
rm trimmed_220721_A00291_0453_AH7JGYDRX2_*_${unique_part}_2.fastq

echo "Aligning sequence files to genome..."
for seqfile in *.fastq; do

    identifier=$(echo $seqfile | cut -f1 -d "." | cut -f8 -d "_")

    echo "Aligning sequence ${unique_part}_${identifier}"

    STAR --genomeDir "$SEQUENCE_PATH/genomes/genom_out" \
	--runThreadN 4 \
	--readFilesIn $seqfile \
	--outFilterType BySJout \
	--outFilterMultimapNmax 20 \
	--outSAMunmapped Within \
	--outFileNamePrefix ${unique_part}_${identifier} \
	--outSAMtype BAM SortedByCoordinate

done

echo "done!"