I am having trouble getting an output file in Rsubreads using featureCounts. I want to set up my data to run analysis of differential expresssion in EdgeR. I'm running about 40 .bam files in series with GRCh38 (genes.gtf) as my reference. I've done this before using Python, but that isn't an option for me right now.
FeatureCounts seems to be running fine with about 5-10 minutes per .bam. It just appears to not create an output file and leaves all the .tmp files in the bin folder.
Using R 4.2.2.
Here is my code
featureCounts(files= c(#It's just 40 .bam files in sequence), annot.ext = #This is GRCh38.gtf, isGTFAnnotationFile=TRUE, GTF.featureType="exon", GTF.attrType="gene_id", isPairedEnd = TRUE, nthreads = 12)