Mapping reads to reference genome

array=("1-1-1-1_S1_L00X" "1-2-1-3_S2_L00X" "1-3-2-1_S3_L00X" "1-4-2-3_S4_L00X" "1-5-3-1_S5_L00X" "1-6-3-3_S6_L00X" "1-7-4-1_S7_L00X" "1-8-4-3_S8_L00X" "1-4B_S7" "2-5B_S10" "3-6B_S13" "4-7B_S16" "5-8B_S19" "6-10B_S22" "7-13B_S1" "8-15B_S4" "9-17B_S8" "10-21B_S11" "11-12M_S14" "12-13M_S17" "13-14M_S20" "15-17M_S23" "16-3T_S2" "17-4T_S5" "18-7T_S9" "19-8T_S12" "20-9T_S15" "21-10T_S18" "22-11T_S21" "23-12T_S24" "24-13T_S3" "25-17T_S6")
for SAMPLE_ID in "${array[@]}"
cat > yourpathtoScriptsDirectory/tophat_${SAMPLE_ID}.slurm <<EOF
#SBATCH --job-name=tophat
#SBATCH --account=uio ## run command projects and see which projects you have access to
#SBATCH --time=20:00:00
#SBATCH --mem-per-cpu=16G
#SBATCH --output=slurm-%j.base

## Set up job environment:
source /cluster/bin/jobsetup
module purge   # clear any inherited modules
set -o errexit

module load tophat/2.0.14
module load bowtie2
module load samtools

# --library-type, -r and --mate-std-dev 118 needs to be adapted to your data, but are also not required options
tophat -G yourpathtoGenome/gff_or_gtf_file.gff -p 8 --library-type fr-firststrand -r 55 --mate-std-dev 118 -o ../Analyses/Mapping/Tophat/${SAMPLE_ID} yourpathtoGenome/bowtie2_index_base_name ../SequenceData/TrimmedSeqs/trimmed_${SAMPLE_ID}_R1_001.fastq.gz ../SequenceData/TrimmedSeqs/trimmed_${SAMPLE_ID}_R2_001.fastq.gz

# Move mapping files from subdirectories, rename and collect under Tophat directory
mv ../Analyses/Mapping/Tophat/${SAMPLE_ID}/accepted_hits.bam ../Analyses/Mapping/Tophat/${SAMPLE_ID}.bam

sbatch yourpathtoScriptsDirectory/tophat_${SAMPLE_ID}.slurm


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