I am unable to follow up the tutorial at https://github.com/mikelove/tximport/blob/master/vignettes/tximport.Rmd
I am getting:
> library(readr) tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v27.csv"))
Error: '/home/mmokrejs/R/x86_64-pc-linux-gnu-library/3.4/tximportData/extdata/tx2gene.gencode.v27.csv' does not exist.
Obviously I do not have the file but where does the tutorial show how to create it?
My aim is to create similar conversion file for ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.transcripts.fa.gz named tx2gene.gencode.v28.csv and continue analysis quant.sf file from Salmon.
I inferred from Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation that I should better use Gencode-based transcriptome than the redundant-one from ENSEMBL. Indeed, I remember seeing warnings during `salmon index` step about duplicate entries.
Thank you for improving the tutorial at the vignette. Ideally also these two which I read but failed to understand/follow-up: