#!/bin/tcsh
#BSUB -J salmonquant_Portfolio_R #job name
#BSUB -n 12 #number of threads
#BSUB -W 5:0 #time for job to complete
#BSUB -R "rusage[mem=0.2]" #to request a node with 0.2 GB of memory
#BSUB -o salmonquant_Portfolio_R.%J.out #output file
#BSUB -e salmonquant_Portfolio_R.%J.err #error file
#to quantify aligned reads using salmon in quasi indexing mode
#set threads under 12 on Hazel
#working directory path is /share/bitcpt/S23/UnityID/Portfolio
#input of aligned reads path is /share/bitcpt/S23/UnityID/Portfolio/AlignedToTranscriptome
#output of aligned reads will go into salmon_align_quant subdirectory in working directory
##########################
# Set the variables
##########################
set SALMON=/usr/local/usrapps/bitcpt/salmon/bin/salmon
set cdna=/share/bitcpt/S23/referenceGenomes/Portfolios/Glycine_max_Lee_v1/glyma.Lee.gnm1_transcriptome.fasta
set IN=AlignedToTranscriptome
##########################
# Gm_YoungLeaf_Rep1
##########################
set s=Gm_YoungLeaf_Rep1
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_YoungLeaf_Rep2
##########################
set s=Gm_YoungLeaf_Rep2
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_YoungLeaf_Rep3
##########################
set s=Gm_YoungLeaf_Rep3
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_YoungLeaf_Rep4
##########################
set s=Gm_YoungLeaf_Rep4
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_YoungLeaf_Rep5
##########################
set s=Gm_YoungLeaf_Rep5
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
#!/bin/tcsh
#BSUB -J salmonquant_Portfolio_RO #job name
#BSUB -n 12 #number of threads
#BSUB -W 5:0 #time for job to complete
#BSUB -R "rusage[mem=0.2]" #to request a node with 0.2 GB of memory
#BSUB -o salmonquant_Portfolio_RO.%J.out #output file
#BSUB -e salmonquant_Portfolio_RO.%J.err #error file
#to quantify aligned reads using salmon in quasi indexing mode
#set threads under 12 on Hazel
#working directory path is /share/bitcpt/S23/UnityID/Portfolio
#input of aligned reads path is /share/bitcpt/S23/UnityID/Portfolio/AlignedToTranscriptome
#output of aligned reads will go into salmon_align_quant subdirectory in working directory
##########################
# Set the variables
##########################
set SALMON=/usr/local/usrapps/bitcpt/salmon/bin/salmon
set cdna=/share/bitcpt/S23/referenceGenomes/Portfolios/Glycine_max_Lee_v1/glyma.Lee.gnm1_transcriptome.fasta
set IN=AlignedToTranscriptome
##########################
# Gm_OldLeaf_Rep1
##########################
set s=Gm_OldLeaf_Rep1
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_OldLeaf_Rep2
##########################
set s=Gm_OldLeaf_Rep2
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_OldLeaf_Rep3
##########################
set s=Gm_OldLeaf_Rep3
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_OldLeaf_Rep4
##########################
set s=Gm_OldLeaf_Rep4
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_OldLeaf_Rep5
##########################
set s=Gm_OldLeaf_Rep5
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
#!/bin/tcsh
#BSUB -J salmonquant_Portfolio_RM #job name
#BSUB -n 12 #number of threads
#BSUB -W 5:0 #time for job to complete
#BSUB -R "rusage[mem=0.2]" #to request a node with 0.2 GB of memory
#BSUB -o salmonquant_Portfolio_RM.%J.out #output file
#BSUB -e salmonquant_Portfolio_RM.%J.err #error file
#to quantify aligned reads using salmon in quasi indexing mode
#set threads under 12 on Hazel
#working directory path is /share/bitcpt/S23/UnityID/Portfolio
#input of aligned reads path is /share/bitcpt/S23/UnityID/Portfolio/AlignedToTranscriptome
#output of aligned reads will go into salmon_align_quant subdirectory in working directory
##########################
# Set the variables
##########################
set SALMON=/usr/local/usrapps/bitcpt/salmon/bin/salmon
set cdna=/share/bitcpt/S23/referenceGenomes/Portfolios/Glycine_max_Lee_v1/glyma.Lee.gnm1_transcriptome.fasta
set IN=AlignedToTranscriptome
##########################
# Gm_SA_Rep1
##########################
set s=Gm_SA_Rep1
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_SA_Rep2
##########################
set s=Gm_SA_Rep2
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_SA_Rep3
##########################
set s=Gm_SA_Rep3
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_SA_Rep4
##########################
set s=Gm_SA_Rep4
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
##########################
# Gm_SA_Rep5
##########################
set s=Gm_SA_Rep5
${SALMON} quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant
The job script should be placed in the working directory following the path:
/share/bitcpt/S23/UnityID/Portfolio
To the run the job:
bsub <"Job name"
To check the job is running:
bjobs
This will produce .quant files which will be copied into a subdirectory for exporting .quant.sf files through globus to upload into Galaxy with DESeq2.
This defines the variable SALMON to call the Salmon software:
set SALMON=/usr/local/usrapps/bitcpt/salmon/bin/salmon
This defines the variable cdna to call the .fasta file of the reference genome:
set cdna=/share/bitcpt/S23/referenceGenomes/Portfolios/Glycine_max_Lee_v1/glyma.Lee.gnm1_transcriptome.fasta
This defines the IN variable to be the path to the AlignedToTranscriptome subdirectory:
set IN=AlignedToTranscriptome
This calls the Salmon software and specifies to use the quantification procedure:
${SALMON} quant
This tells Salmon to infer the library type automatically:
-l A
This is the input for the created STAR alignment file:
-a ${IN}/${s}_Aligned.toTranscriptome.out.bam
This specifies the file of the transcriptome targets file:
--targets ${cdna}
(uses genome wide transcriptome file instead of genome assembly for reference mapping)
This specifies what to name the output and where to save it using an output flag:
-o salmon_align_quant/${s}.quant