RNA-Seq Read Counts for SCAN.UPC
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Jo ▴ 30
@jo-8608
Last seen 8.2 years ago

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.

 

scan.upc rnaseq • 1.2k views
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@stephen-piccolo-6761
Last seen 3.5 years ago
United States

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.

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