6_diff_expresion.txt

#warming_AK

#Adriana L. Romero-Olivares' protocol for processing RNAseq data of soil 
#Section 6 
#File name: 6_diff_expresion
#Step: Differential expression analysis 

#using Trinity's toolkit run differential expression analysis using edgeR and the script "run_DE_analysis.pl"  

module load trinity/r2016-2.3.2
module load R/3.3.2

/data/apps/trinity/r2016-2.3.2/Analysis/DifferentialExpression/run_DE_analysis.pl --matrix matrix.counts.matrix --method edgeR --min_reps_min_cpm 1,1 --dispersion 0.4    

#next, analyze differential expression data with Trinity's toolkit script "analyze_diff_expr.pl" 

module load trinity/r2017-2.4.0
module load R/3.3.2

/data/apps/trinity/r2017-2.4.0/Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix matrix.TMM.EXPR.matrix -P 0.05 --output express_DF_0.05  

#table with up and down regulated genes significant at p = 0.05 are in folder express_DF_0.05

#next, proceed to identify contigs down and up regulated using annotated meta-transcriptome.