Hello,

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)

featureCounts doesn't create output files. Instead it works in the usual way for functions in R, meaning that it creates an R object that you can save and manipulate at the R level, for example:

fc <- featureCounts( ... )

See help("featureCounts") for detailed information about the output. You could for example convert the featureCounts output to an edgeR DGEList object by:

library(edgeR)
y <- featureCounts2DGEList(fc)

featureCounts generally deletes all temporary files on completion. If tmp files remain, then it may be that the featureCounts has not completed successfully.