hisat2_rnaseq_single.pbs

#!/bin/bash
#PBS -l nodes=1:ppn=28
#PBS -l mem=112gb
#PBS -l walltime=20:00:00
#PBS -A PCON0005
cd $PBS_O_WORKDIR

module load samtools/1.6

module load hisat2/2.1.0

#/fs/project/PCON0005/BISR/programs/FastQC_0.11.7/fastqc  -o  fastqc_out $R1


#NOTE: run with --dta if you intend to use stringtie later

#REF=$REF
#hisat2 -p 12 --new-summary --summary-file $OUTPUT.hisat2.summary -x $REF -U $R1  -S $OUTPUT.sam

#1-Convert sam to bam
#samtools view -bS -o $OUTPUT.bam $OUTPUT.sam

# 2- Sort bam file
#samtools sort $OUTPUT.bam  -o $OUTPUT.sorted.bam

# 3- Generate index for bam file
#samtools index $OUTPUT.sorted.bam


module load R/3.5.0
module load python/2.7
export PYTHONPATH=/users/PAS1208/osu0972/.local/lib/python2.7/site-packages
export PATH=$PATH:/users/PAS1208/osu0972/.local/bin

#RIBOBED=/fs/project/PCON0005/BISR/reference/HISAT2/Homo_sapiens/grch38/GRCh38_rRNA.bed
#BED=/fs/project/PCON0005/BISR/reference/HISAT2/Homo_sapiens/grch38/hg38_GENCODE_v23.bed

junction_annotation.py -i $OUTPUT.sorted.bam -o $POSTALN_OUT\_junc -r $BED
read_distribution.py  -i $OUTPUT.sorted.bam -r $BED > $POSTALN_OUT\_readdist
infer_experiment.py -r $BED -i $OUTPUT.sorted.bam > $POSTALN_OUT\_infer
split_bam.py -i $OUTPUT.sorted.bam  -r $RIBOBED -o $POSTALN_OUT\_ribo

java -Xmx4g  -jar /fs/project/PCON0005/BISR/programs/picard-tools-2.4.1/picard.jar CollectInsertSizeMetrics I=$OUTPUT.sorted.bam  O=$POSTALN_OUT.insert_size_metrics.txt H=$POSTALN_OUT.insert_size_histogram.pdf M=0.5 VALIDATION_STRINGENCY=LENIENT

java -Xmx4g   -jar /fs/project/PCON0005/BISR/programs/picard-tools-2.4.1/picard.jar MarkDuplicates I=$OUTPUT.sorted.bam  O=$POSTALN_OUT.marked_duplicates.bam M=$POSTALN_OUT.marked_dup_metrics.txt VALIDATION_STRINGENCY=LENIENT

/fs/project/PCON0005/BISR/programs/subread-1.5.1/bin/featureCounts -a $GTF   --primary   -o $FEATURE_OUTPUT.featurecounts $OUTPUT.sorted.bam


#/fs/project/PCON0005/BISR/programs/subread-1.5.1/bin/featureCounts -a $GTF   -s 2 --primary -p   -o $FEATURE_OUTPUT.featurecounts $OUTPUT.sorted.bam