Summerizing Mapped Reads

Question

[HNK]

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.

Answer 1

[Devon Ryan]

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