While aligning RNA-Seq data and quantifying the actual number of reads mapped to my transcriptome, I realised that samtools flagstat does not report the actual alignied reads stats. I used RSEM for my alignment and expression calculation. I am aware the samtools counts secondary alignments thereby increasing total number of reads that pass QC and therefore influence the alignment percentage that it throws as the output. Source here
Is there any other tool that can precisely give the actual number of reads correctly mapping in pairs to the transcriptome? Somewhat like the log.out file in STAR does.