-reading file: uninfected_01/quant.sf
-reading file: infected_01/quant.sf
-reading file: infected_02/quant.sf
-reading file: infected_03/quant.sf
-reading file: infected_04/quant.sf
-reading file: infected_05/quant.sf
-reading file: infected_06/quant.sf
-reading file: uninfected_02/quant.sf
-reading file: uninfected_03/quant.sf
-reading file: infected_07/quant.sf
-reading file: infected_08/quant.sf
-reading file: infected_09/quant.sf
-reading file: infected_10/quant.sf
-reading file: infected_11/quant.sf
-reading file: infected_12/quant.sf
-reading file: infected_13/quant.sf
-reading file: uninfected_04/quant.sf
-reading file: uninfected_05/quant.sf
-reading file: infected_14/quant.sf
-reading file: infected_15/quant.sf
-reading file: infected_16/quant.sf
-reading file: infected_17/quant.sf
-reading file: infected_18/quant.sf
-reading file: uninfected_06/quant.sf


* Outputting combined matrix.

/gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix salmon.isoform.TPM.not_cross_norm > salmon.isoform.TMM.EXPR.matrixCMD: R --no-save --no-restore --no-site-file --no-init-file -q < salmon.isoform.TPM.not_cross_norm.runTMM.R 1>&2 
> library(edgeR)
Loading required package: limma
> 
> rnaseqMatrix = read.table("salmon.isoform.TPM.not_cross_norm", header=T, row.names=1, com='', check.names=F)
> rnaseqMatrix = as.matrix(rnaseqMatrix)
> rnaseqMatrix = round(rnaseqMatrix)
> exp_study = DGEList(counts=rnaseqMatrix, group=factor(colnames(rnaseqMatrix)))
> exp_study = calcNormFactors(exp_study)
> exp_study$samples$eff.lib.size = exp_study$samples$lib.size * exp_study$samples$norm.factors
> write.table(exp_study$samples, file="salmon.isoform.TPM.not_cross_norm.TMM_info.txt", quote=F, sep="\t", row.names=F)
> 
/gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix salmon.gene.TPM.not_cross_norm > salmon.gene.TMM.EXPR.matrixCMD: R --no-save --no-restore --no-site-file --no-init-file -q < salmon.gene.TPM.not_cross_norm.runTMM.R 1>&2 
> library(edgeR)
Loading required package: limma
> 
> rnaseqMatrix = read.table("salmon.gene.TPM.not_cross_norm", header=T, row.names=1, com='', check.names=F)
> rnaseqMatrix = as.matrix(rnaseqMatrix)
> rnaseqMatrix = round(rnaseqMatrix)
> exp_study = DGEList(counts=rnaseqMatrix, group=factor(colnames(rnaseqMatrix)))
> exp_study = calcNormFactors(exp_study)
> exp_study$samples$eff.lib.size = exp_study$samples$lib.size * exp_study$samples$norm.factors
> write.table(exp_study$samples, file="salmon.gene.TPM.not_cross_norm.TMM_info.txt", quote=F, sep="\t", row.names=F)
>