FeatureCount parameters

[Yippee3]

Why is the Successfully assigned alignments so low 37.3% when i use featureCounts -f -O -p -s 2 -T 16 -F GTF -a ../vm25self.DEXSeq.gtf -o ../vm25selfallDEXSeqcount.txt test1.sort.bam test2.sort.bam what is more, my data is paired-end, but commandline display The reads are assigned on the single-end mode

Process BAM file test1.sort.bam... || || Strand specific : reversely stranded || || Paired-end reads are included. || || The reads are assigned on the single-end mode. || || Total alignments : 106372557 || || Successfully assigned alignments : 39673738 (37.3%) || || Running time : 0.18 minutes

Thanks a lot