Question: Inferring Inter-individual variation using only merged raw read counts of the individual genes ?
gravatar for sandKings
2.0 years ago by
sandKings10 wrote:

Hi all!

I need some help to look at inter-individual gene variation in an RNA-Seq dataset of 20 patients. I am interested in variation in 5 genes. The only raw data I have is the merged raw read counts of the individual genes for all the 20 samples. 8 samples are from T1, 6 samples from T2 and 6 samples from T3 where T is treatment. I did a DESEq2/EdgeR analysis and I have a list of differentially expressed genes using the counts file provided. These samples are from 3 different treatments and are not paired, as in, they're not from same patients (pre vs post treatment).

Is there any way to accomplish this? Thanks!

rna-seq • 451 views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by sandKings10

So you only have the total counts from all patients, not the counts per patient? Do you have the full output of DESeq2 or edgeR? If so, could you post a few lines?

ADD REPLYlink written 2.0 years ago by h.mon30k
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