Alignment

After indexing the reference genome, alignment of the reads will take place. For future use, replace sections in bold to adjust the code as needed.

#!/bin/tcsh

#BSUB -J staralign_W-CCV-YL #job name

#BSUB -n 12 #number of threads

#BSUB -W 10:0 #time for job to complete

#BSUB -R span[hosts=1] #to keep tasks on one node

#BSUB -R "rusage[mem=0.2]" #to request a node with 20MB of memory

#BSUB -o staralign_Portfolio_%J.out #output file

#BSUB -e staralign_Portfolio_%J.err #error file

#Script to align RNA-seq reads to indexed genome using STAR

#STAR cannot make use of HPC MPI, must have -R options to set 1 node & memory

#set threads under 12 on Hazel

#input of indexed genome path is /share/bitcpt/S23/cacofre/Protfolio/starindices

#input of sequence reads path is /share/bitcpt/S23/RawData/Glycine_max/

#output of aligned reads will go into AlignedToTranscriptome subdirectory in working directory

# SET SCRIPT VARIABLES

set STAR=/usr/local/usrapps/bitcpt/star/bin/STAR

set IN=/share/bitcpt/S23/RawData/Glycine_max

set index=starindices

set out=AlignedToTranscriptome

################################

#Young Leaf Rep 1

################################

set S=Gm_YoungLeaf_Rep1

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#Young Leaf Rep 2

################################

set S=Gm_YoungLeaf_Rep2

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#Young Leaf Rep 3

################################

set S=Gm_YoungLeaf_Rep3

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#Young Leaf Rep 4

################################

set S=Gm_YoungLeaf_Rep4

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#Young Leaf Rep 5

################################

set S=Gm_YoungLeaf_Rep5

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

#!/bin/tcsh

#BSUB -J staralign_W-CCV-SA #job name

#BSUB -n 12 #number of threads

#BSUB -W 10:0 #time for job to complete

#BSUB -R span[hosts=1] #to keep tasks on one node

#BSUB -R "rusage[mem=0.2]" #to request a node with 20MB of memory

#BSUB -o staralign_Portfolio_SA%J.out #output file

#BSUB -e staralign_Portfolio_SA%J.err #error file

#Script to align RNA-seq reads to indexed genome using STAR

#STAR cannot make use of HPC MPI, must have -R options to set 1 node & memory

#set threads under 12 on Hazel

#input of indexed genome path is /share/bitcpt/S23/cacofre/Protfolio/starindices

#input of sequence reads path is /share/bitcpt/S23/RawData/Glycine_max/

#output of aligned reads will go into AlignedToTranscriptome subdirectory in working directory

# SET SCRIPT VARIABLES

set STAR=/usr/local/usrapps/bitcpt/star/bin/STAR

set IN=/share/bitcpt/S23/RawData/Glycine_max

set index=starindices

set out=AlignedToTranscriptome

################################

#SA Rep 1

################################

set S=Gm_SA_Rep1

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#SA Rep 2

################################

set S=Gm_SA_Rep2

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#SA Rep 3

################################

set S=Gm_SA_Rep3

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#SA Rep 4

################################

set S=Gm_SA_Rep4

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

# SA Rep 5

################################

set S=Gm_SA_Rep5

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

#!/bin/tcsh

#BSUB -J staralign_W-CCV-SA #job name

#BSUB -n 12 #number of threads

#BSUB -W 10:0 #time for job to complete

#BSUB -R span[hosts=1] #to keep tasks on one node

#BSUB -R "rusage[mem=0.2]" #to request a node with 20MB of memory

#BSUB -o staralign_Portfolio_SA%J.out #output file

#BSUB -e staralign_Portfolio_SA%J.err #error file

#Script to align RNA-seq reads to indexed genome using STAR

#STAR cannot make use of HPC MPI, must have -R options to set 1 node & memory

#set threads under 12 on Hazel

#input of indexed genome path is /share/bitcpt/S23/cacofre/Protfolio/starindices

#input of sequence reads path is /share/bitcpt/S23/RawData/Glycine_max/

#output of aligned reads will go into AlignedToTranscriptome subdirectory in working directory

# SET SCRIPT VARIABLES

set STAR=/usr/local/usrapps/bitcpt/star/bin/STAR

set IN=/share/bitcpt/S23/RawData/Glycine_max

set index=starindices

set out=AlignedToTranscriptome

################################

#SA Rep 1

################################

set S=Gm_SA_Rep1

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#SA Rep 2

################################

set S=Gm_SA_Rep2

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#SA Rep 3

################################

set S=Gm_SA_Rep3

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

#SA Rep 4

################################

set S=Gm_SA_Rep4

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM

################################

# SA Rep 5

################################

set S=Gm_SA_Rep5

set EN=fq.gz

echo ${IN}/${S}_1.${EN}

${STAR} --runThreadN 12 --runMode alignReads --genomeDir ${index} --outFileNamePrefix ${out}/${S}_ --readFilesIn ${IN}/${S}_1.${EN} ${IN}/${S}_2.${EN} --readFilesCommand zcat --outSAMtype BAM Unsorted --twopassMode Basic --quantMode TranscriptomeSAM