How to get DESeq2 results in large count matix files?
1
0
Entering edit mode
@mathavanbioinfo-11955
Last seen 2 days 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 • 674 views
ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
@mikelove
Last seen 11 hours ago
United States

Cross posted and answered on GitHub.

ADD COMMENT

Login before adding your answer.

Traffic: 792 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6