From 2b0d423e904882ff47d4ba5822cbe1402a94d5ec Mon Sep 17 00:00:00 2001 From: mikelove Date: Wed, 29 Aug 2018 13:07:20 -0400 Subject: [PATCH] add note --- DESCRIPTION | 2 +- vignettes/rnaseqDTU.Rmd | 13 +++++++++++++ 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b1c5f9c..a3a51c6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: rnaseqDTU Title: RNA-seq workflow for differential transcript usage following Salmon quantification -Version: 0.99.18 +Version: 0.99.19 Date: 2018-06-27 Authors@R: c(person(role=c("aut", "cre"), "Michael", "Love", email = "michaelisaiahlove@gmail.com"), person(role=c("aut"), "Charlotte", "Soneson"), diff --git a/vignettes/rnaseqDTU.Rmd b/vignettes/rnaseqDTU.Rmd index 49748b9..1a033e0 100644 --- a/vignettes/rnaseqDTU.Rmd +++ b/vignettes/rnaseqDTU.Rmd @@ -433,6 +433,19 @@ described by @Trapnell2013Differential and @Soneson2015Differential. Our DTU and DGE `countsFromAbundance` recommendations are summarized in Figure \@ref(fig:diagram). +A final note is that, the motivation for using `scaledTPM` counts +hinges on the fact that estimated fragment counts scale with +transcript length in fragmented RNA-seq data. If a different experiment +is performed and a different quantification method used to produce +counts per transcript which *do not* scale with transcript length, +then the recommendation would be to use these counts per transcript directly. +Examples of experiments producing counts per transcript that would potentially +not scale with transcript length include +counts of full-transcript-length or nearly-full-transcript-length reads, +or counts of 3' tagged RNA-seq reads aggregated to transcript groups. +In either case, the statistical methods for DTU could be provided directly +with the transcript counts. + The following code chunk is what one would use in a typical analysis, but is not evaluated in this workflow because the quantification files are not provided in the *rnaseqDTU* package due to size restrictions.