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?
Even if do not have access to the original bams, you can easily grab single-end fastq (in which case you will have to align) and / or bam files, and run featureCounts twice, withand without
-p. The result of this test will tell you if your original counts are correct or not.
You don't want to submit potentially bogus results to GEO (with your name on it) based on "but this internet guy told me my counts were fine", do you?
I doubt it will matter. When you have paired end reads, you need the software to understand that if it sees the same read name twice; one read1 and on read2, aligning to the same gene twice, it has to not count those as two separate reads, since they came from one fragment.
That won't be a problem with a single end dataset.