Hi! I'm new in the bioinformatic world so, maybe, this is commonly known in the comunity but I couldn't find anything in the RSubread package instructions...
I know that featureCounts have an in-built hg38 genome. For most of my purposes it works great but I have some Immunoprecipitation and RNAseq of a protein that bind to the 3'UTR of the mRNA. I would like to try to compare the hg38 results with a counting only for the 3'UTR. I get the 3'UTR genome from Table Borwser at UCSC (in fasta format) and I specify in featureCounts the option "genome" for my 3'UTR file.
Although fC does not report any error, I couldn't find any differences in the countings when I compared the 3'UTR results with hg38 results. What I am doing wrong?
Here is the command line for fC:
fc <- featureCounts(files=targets$InputFile,annot.inbuilt="hg38",genome = "hg38_3UTR.fa")