How to get DESeq2 results in large count matix files?
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@mathavanbioinfo-11955
Last seen 7 months ago
India

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!!!

DESeq2 BiocParallel MulticoreParam • 945 views
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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?

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Note that this was posted twice. I’ve answered on GitHub.

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@mikelove
Last seen 17 hours ago
United States

Cross posted and answered on GitHub.

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