https://divingintogeneticsandgenomics.com/tags/deseq/ Recent content in DESeq on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Fri, 01 Nov 2013 19:57:00 -0700 https://divingintogeneticsandgenomics.com/archive/deseq-work-flow/ Fri, 01 Nov 2013 19:57:00 -0700 https://divingintogeneticsandgenomics.com/archive/deseq-work-flow/ I was working on a human RNA-seq data set, and I already got the count matrix by HTSeq. see my previous post here RNA-seq analysis samtools sort and htseq-count Now, I am ready to use DESeq to detect the differentially expressed genes. I followed the nature protocol from Simon Anders and here http://dwheelerau.com/2013/04/15/how-to-use-deseq-to-analyse-rnaseq-data/ for more details read the DESeq manual. View this gist on GitHub several out put > head(countsTable) a1 b1 a2 b2 a3 b3 0R7H2P 21 9 3 6 1 4 5S_rRNA 55 87 56 56 34 40 7SK 171 89 61 84 57 47 A1BG 15 34 38 10 12 23 A1BG-AS1 65 49 140 41 40 44 A1CF 293 109 417 90 181 84 > head(counts(cds,normalized=TRUE)) a1 b1 a2 b2 a3 0R7H2P 14.