Dear All I am working on a denovo transcriptome analysis of the sugar cane plant. The count matrix has a 1792064 number of transcripts. Now, the differential gene expression is running by the tools DESeq2. The total number of samples is 36 and it has 12 groups comparison. The differential gene expression has been running for more than 25 days to date. Some files are generated in the data folder
readCountRlogNorm.xls rlog_Normalized_Values.txt readCountNorm.xls
and the figure folder SampleDistanceRlog.pdf SampleCorrelationRlog.pdf PCA.png
absPairVenn folder showing empty
Please check the library used in the script. library(DESeq2) library("BiocParallel") register(MulticoreParam(100))
Command used Rscript DEseq2_replicate.R counts.matrix SampleInfo_Replicates contrast
Please help me!!!
Well, save to say something is very wrong here. Can you show the content of that script? is it intentional that you compare transcripts and not genes?
Note that this was posted twice. I’ve answered on GitHub.