2_STAR.pbs

#PBS -N STAR.2.6.0c_map
#PBS -M johndou@umich.edu
#PBS -m abe
#PBS -j oe
#PBS -V

#PBS -q fluxod
#PBS -A bakulski_fluxod
#PBS -l qos=flux

#PBS -l nodes=1:ppn=6:largemem,mem=64gb,walltime=72:00:00 

cat $PBS_NODEFILE

module load samtools

for path in /nfs/turbo/bakulski1/Datasets/Padmanabhan/ruddle.brcf.med.umich.edu/Run_2742/padmanabha/Sample_124*; do
	
	SAMPLEID="$(basename "${path}")"
	
	rm -r /nfs/turbo/bakulski1/People/johndou/vsheep/Run_2742/STAR/$SAMPLEID/
	mkdir /nfs/turbo/bakulski1/People/johndou/vsheep/Run_2742/STAR/$SAMPLEID/
 
	for file in $path/*.fastq.gz; do
    FASTQF="$(basename "${file}")"
    PREFIX=${FASTQF//.fastq.gzAligned.out.sam/}
    
	  /nfs/turbo/bakulski1/Software/STAR/bin/Linux_x86_64_static/STAR \
  	--genomeDir /nfs/turbo/bakulski1/People/johndou/Sheep_Genome/refSTAR/ \
  	--readFilesIn \
  	/nfs/turbo/bakulski1/Datasets/Padmanabhan/ruddle.brcf.med.umich.edu/Run_2742/padmanabha/$SAMPLEID/$FASTQF \
  	--readFilesCommand gunzip -c \
  	--runThreadN 6 \
  	--clip5pNbases 0 3 \
  	--outFilterMultimapNmax 10 \
  	--outSAMmode Full \
  	--sjdbScore 2 \
  	--outFileNamePrefix \
  	/nfs/turbo/bakulski1/People/johndou/vsheep/Run_2742/STAR/$SAMPLEID/$PREFIX \
  	--outReadsUnmapped Fastx
   
   done

done