Salmon Quantification

1. Copy the index script from the Tom directory into the Portfolio directory

#make sure you are in the Portfolio directory

cp /share/bitcpt/Fall2022/lscapozi/Tom/Tom.salmon.sh .

2. Rename the file to reflect the Tom-Heinz1706 data

mv Tom.salmon.sh Hz.salmon.sh

3. Edit the script

#!/bin/tcsh

#BSUB -J salmonquant_Tom #job name

#BSUB -n 12 #number of threads

#BSUB -W 5:0 #time for job to complete

#BSUB -R "rusage[mem=20000]" #to request a node with 20MB of memory

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

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

#to quantify aligned reads using salmon in quasi indexing mode

#set threads under 12 on Henry2

#working directory path is /share/bitcpt/Fall2022/lscapozi/Portfolio

#input of aligned reads path is /share/bitcpt/Fall2022/lscapozi/Portfolio/AlignedToTranscriptome

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

module load conda

conda activate /usr/local/usrapps/bitcpt/salmon

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

# Set the variables

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

set cdna=/share/bitcpt/Fall2022/referenceGenomes/Solanum_lycopersicum/Portfolio/Tom-Heinz1706/Tom-Heinz_transcriptome.fasta

set IN=/share/bitcpt/Fall2022/lscapozi/Portfolio/AlignedToTranscriptome

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

# Sl-Leaf 1

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

set s=Sl_Leaf_Rep1_3X

salmon quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant

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

# Sl-Leaf 2

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

set s=Sl_Leaf_Rep2_3X

salmon quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant

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

# Sl-Leaf 3

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

set s=Sl_Leaf_Rep3_3X

salmon quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant

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

# Sl-SAM 1

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

set s=Sl_SAM_Rep1_3X

salmon quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant

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

# Sl-SAM 2

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

set s=Sl_SAM_Rep2_3X

salmon quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant

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

# Sl-SAM 3

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

set s=Sl_SAM_Rep3_3X

salmon quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant

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

# Sl-SAM 4

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

set s=Sl_SAM_Rep4_3X

salmon quant -l A -a ${IN}/${s}_Aligned.toTranscriptome.out.bam --targets ${cdna} -o salmon_align_quant/${s}.quant

echo Done

4. Run the Salmon Quantification of the Tom-Heinz1706 code

bsub <Hz.salmon.sh

5. Check the output

ll salmon_align_quant