Hi,
I have a set of bam files for my samples and I just want to align them to the e coli reference genome to get non-normalised unique reads for each gene. I am trying to do this using summarizeOverlaps (as I'm using R and I don't have a mac for featurecounts) and I have looked at the example on bioconductor as follows:
(ebg <- exonsBy(txdb, by="gene"))
se <- summarizeOverlaps(features=ebg, reads=bamfiles,
mode="Union",
singleEnd=FALSE,
ignore.strand=TRUE,
fragments=TRUE )
I don't really understand how my code will differ for the E coli genome compared to the example; what if I don't have introns of exons and just want to align to each gene? What do I write/create for "features="?
I assume I keep the "Union" mode as shown in Fig 1 of the vignette? Are there other optional modes?
As my data is single ended, I assume I also put true and do not put anything for ignore.strand or fragments if singleEnd=TRUE?
So far my code is:
(ebg <- exonsBy(txdb, by="gene"))
se <- summarizeOverlaps(features=ebg, reads=bamfiles,
mode="Union",
singleEnd=FALSE)
Is this correct or do I need to change ebg?
I've searched through the forum and still can't understand, sorry.
Thanks for your help.