[BioC] Counting reads for edgeR or voom()

[Cittaro Davide]

Hi all, just a quick question on best practices to create datasets for RNA-seq analysis with edgeR or limma:::voom().
I must create a table in which read counts for every entity (i.e. every transcript) for every sample. In order to do this I have at least a couple of options that may affect results:
1- should I count all reads overlapping the whole transcript or the reads that overlap exons?
2- should I use every transcript or just the primary one?

Thanks

d

/*
Davide Cittaro, PhD

Coordinator of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
Ospedale San Raffaele
Via Olgettina 58
20132 Milano
Italy

Office: +39 02 26439140
Mail: cittaro.davide at hsr.it
Skype: daweonline
*/












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