Summerizing Mapped Reads
hello i have been new in RNA-seq , and have read alot of papers on this RNA-seq approach. i wanted to know if some one can provide me with any test/sample summarize read counts file. I just want to try normalizing that and perform the DE test in order to get the list of differentially expressed genes.
1 answer
Just use the pasilla dataset from Bioconductor:
library("pasilla")
library("DESeq2")
data("pasillaGenes")
>head(counts(pasillaGenes))
treated1fb treated2fb treated3fb untreated1fb untreated2fb
FBgn0000003 0 0 1 0 0
FBgn0000008 78 46 43 47 89
FBgn0000014 2 0 0 0 0
FBgn0000015 1 0 1 0 1
FBgn0000017 3187 1672 1859 2445 4615
FBgn0000018 369 150 176 288 383
untreated3fb untreated4fb
FBgn0000003 0 0
FBgn0000008 53 27
FBgn0000014 1 0
FBgn0000015 1 2
FBgn0000017 2063 1711
FBgn0000018 135 174
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