RNAseq analysis: I have read counts for all CDS. Could I use standard methods (limma-voom, edgeR) for DEA??

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2.3 years ago

Elena • 0

Hi all,

I have read counts for all the cds in the new version of the human genome. The mapping was done to the genome and then, the counts were calculated using cds. I was wondering if I could use standard methods for doing Differential Expression Analysis. Could you point me to some references?

Thank you in advance!

RNAseq DGE CDS mapping DEA • 403 views

ADD COMMENT • link updated 2.3 years ago by ATpoint 85k • written 2.3 years ago by Elena • 0

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That's a bit unusual. CDS is not precise as large parts of a given CDS can be shared among transcripts of the same genes. Can you say what precisely the setup is? It would likely be better/more standard/more reliable to simply quantify your data against the entire transcriptome.

ADD REPLY • link 2.3 years ago by ATpoint 85k

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