Salmon quantification code

Salmon normalization and quantification tool

Transcripts per million or TPM metric is used for normalization eliminating the bias of less depth of sequences and shorter length of sequences. Salmon is the quantification tool that produces the counts for each sequence referred to as the read counts.

Quantification of the aligned sequences producing the quant.sf file for each sample which is converted to txt files and used for differential expression analysis

Script below:

#!/bin/tcsh

#BSUB -J salmonquant_Portfolio #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_Portfolio.%J.out #output file

#BSUB -e salmonquant_Portfolio.%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/maharry/Portfolio

#input of aligned reads path is /share/bitcpt/Fall2022/maharry/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/Pot-Landrace/Diploid-potato_

transcriptome.fasta

set IN=/share/bitcpt/Fall2022/maharry/Portfolio/AlignedToTranscriptome (path to input files)

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

# Sl-Leaf 1

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

set s=Sl_Leaf_Rep1_3X