I got a list of paired end bam files, and want to do DESeq2 analysis. The first thing is to count the reads at gene level. I tried feature counts. However, it requires reorder of the bam files if I specified paired end is True, which takes infinite time for my huge dataset. I also tried summarizeOverlaps, which also takes very long time.
Is there any tools could quickly count the paired end reads for DESeq2 at gene level? Thanks.