Entering edit mode
7.9 years ago
Pfs ▴ 550
I am having trouble to understand the results of the counting in SummarizeOverlap vignette, which implements the methods in HTSeq.
Has anybody tried to work the example out manually? It may sound tedious, but I wanted to make sure I understand how to interpret the results.
For example, why the results for method = Union report 1 read for feature C? The read also overlap with feature G, so it should be discarded.
I could paste the code, if that helps. The vignette is available here: http://www.bioconductor.org/packages/release/bioc/vignettes/GenomicAlignments/inst/doc/summarizeOverlaps.pdf