I have paired-end RNAseq data, and I used STAR aligner to do alignment, so basically for each paired-end fastq files I ended-up creating one alignment file (bam). Now I would like to create a count matrix to do DE analysis. I would like to use featureCounts tool. I was wondering what are the optimal flags to use? I am not sure if I have to use -p flag, since my reads are already aligned to the reference.