I have a basic question in trying to make sense of the number of reads mapped by tophat. My understanding is the following
#input_reads (to tophat) = #unmapped_reads(by tophat) + #primary_mapped reads
In my case the above equation is not working out as #primarymapped reads + #unmappedreads is coming out to be more than #input_reads. My hunch is that either the flag is not correctly set in the bam file by tophat or my equation/understanding of how the tophat uses & flags the reads is not right.
Also I am calculating the #primary reads by using the sam flag -F 256