How to use normalized DESeq2 data for downstream analysis?
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Arying • 0
@arying-15699
Last seen 5.9 years ago

Hi all,

I am getting some RNAseq data from my colleague and it only has the DESeq2 normalized counts. Are there any ways that I could utilize these data for downstream analysis in DESeq2? 

Thanks!

deseq2 normalization • 620 views
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@mikelove
Last seen 3 hours ago
United States

Ask for the original counts. This is the point of using a count based method, which take into account variability in sequencing depth across genes and samples.

In my experience, 99% of the time someone can obtain the original counts for you. It's very uncommon for bioinformatic groups to perform quantification (either alignment or alignment-free), and then delete the data that was used to produce the original count table. 

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