Inferring Inter-individual variation using only merged raw read counts of the individual genes ?
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5.9 years ago
sandKings ▴ 40

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 • 840 views
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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?

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