Hello,

I am trying to generate RNA-Seq read counts for an RNA-Seq dataset from the NCBI site. I am then going to use the read count files to run a UPC normalization on the dataset using SCAN.UPC. 

How can I obtain RNA-Seq read count files using R?

Please advise.

Hi Jo,

Thanks for your question. Are you familiar with using read aligners to map RNA-Seq data to a reference genome. In the past, I have had success using the Rsubread package. You can find some example code here: https://github.com/srp33/TCGA_RNASeq_Benchmark

But there are many other such tools that can be used. https://en.wikipedia.org/wiki/List_of_RNA-Seq_bioinformatics_tools

You'd just want to be careful that you use read-count output (rather than RPKM/FPKM) as input to UPC.