I am looking through an old pipeline that was run over a year ago in preparation for submitting data to GEO. I discovered that although the sequencing in this experiment was single-read (vs. paired-end), I had run featureCounts in paired-end mode (with a parameter of -p). According to the featureCounts documentation, the -p flag has the following definition: "If specified, fragments (or templates) will be counted instead of reads. This option is only applicable for paired-end reads." Did adding this parameter by mistake affect the run at all? Or did it not matter as all samples were single-read anyway?