I am doing a featureCounts on 4 RNA-seq samples, code as found below. I am counting on the "gene" from gencode v33 as seen in the gtf file. Reason why I am doing this is to counter-check the counting process against the aligner's (STAR in this case) summary output.
featureCounts -a gencode.v33.primary_assembly.annotation.gtf -o out.txt -O --fraction -B -t "gene" -s 2 -T 8 --primary -p 504-709_S21Aligned.sortedByCoord.out.bam 504-710_S22Aligned.sortedByCoord.out.bam 505-702_S26Aligned.sortedByCoord.out.bam 505-703_S27Aligned.sortedByCoord.out.bam
Am I right to assume that the above code will correspond to the uniquely mapped reads summary in STAR? The counting above is very close but not exactly same to the reported uniquely mapped reads from STAR, hence my assumption.
If so, what does the --primary tag do in this case, as I assume it will count the multi-mapped reads which is given a primary tag.