I am attempting to create a txdb and tx2gene for Sus scrofa transcipts.
I am struggling map my salmon transcript quant.sf files to my genome. I am using the transcript file from https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000003025.6/, and tried to create a TxDb from the genomic sequence fast file, GFF3 and GTF. My IDs never seem to match and I am unsure how to fix this as I am pulling both files from the same site. I have also tried using the TxDb UCSC susScr11 ref genome but I get the same non-matching IDs.
Code should be placed in three backticks as shown below
# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session
sessionInfo( )