a quick question:
After running Tophat with a fastQ files, I found the # of reads from (accepted_hits.bam and unmapped.bam) is greater than the # of reads in fastQ file. Why is this? I thought the accepted_hits.bam plus unmapped should add up to the total # of reads that tophat started with.
I use samtools view -c to count the total reads in both accepted_hits.bam and unmapped.bam, and used grep "^@" to count the # of reads in fastQ file.