I was trying to start an scRNAseq experiment by generating a count matrix with Rsubread. This is using RStudio Version 1.1.453 and R3.6.1. On a Windows 10 machine. The tutorial to start the project works perfectly:
library(Rsubread) ref <- system.file("extdata","reference.fa",package="Rsubread") buildindex(basename="reference_index",reference=ref)
Everything runs exactly as it says in the vignette at: https://bioconductor.org/packages/3.10/bioc/vignettes/Rsubread/inst/doc/Rsubread.pdf
But my reference genome from NCBI (concatenated into one file) gives an error when building the index.
ref <- system.file("extdata","cat9ref.fa",package="Rsubread") buildindex(basename="reference_index",reference=ref) Error in normalizePath(path.expand(path), winslash, mustWork) : path="": The filename, directory name, or volume label syntax is incorrect
I'm fairly new to R, but this looks like a formatting error. Couldn't find anything by google that helped. Hopefully someone has seen this and can tell me what I'm doing wrong. Thanks Pete