Edger To Find De And Non-De Reads

Question

[joanne.lee]

I’m using EdgeR to find differentially expressed reads within 100bp windows. To help my analysis later on I’d like EdgeR to give me an output that contains every 100bp window I have regardless of if it’s differentially expressed or not. I have done my analysis similar to that of example 4.3 in the EdgeR user's guide

Any help on how to get the expression data back from my total 2393345 windows would be appreciated.

Thanks

[Irsan]

Few things I don't understand:

1) "Differentially expressed reads". Reads are not expressed, so they certainly cannot be differentially expressed. You mean genes/transcripts?

2) "within 100bp windows". Why do you summarize RNA-data (at least, I guess you are talking about RNA data) in windows? You mean genomic windows? You should summarize RNA-data by transcript / gene entities

Maybe your question is: "I have mapped my RNA-seq to a reference genome, how can I get a table that summarizes the amount of reads mapped to each gene, for each sample seperately"?

[Nicolas Rosewick]

Do you have already infer your count matrix from the alignment ?

Answer 1

[Sean Davis]

You could use topTags() and set n to a very large number. If you need to sort by something else, just assign the result of topTags to a variable (it is a data.frame) and sort to your heart's content.