I ran my data using Tophat2, for the "-r" and "--mate-std-dev", I left them as default value.
Next, I watch the paired-end reads in Savant Genome Browser, I check the insetsize for the paired reads, they are so variant.
As default, insersize should in the range of 50(+- 20), from 30~70. But I found many insersize bigger than 200nt, or overlapping.
Why the default value didn't work? The default is randomized insertsize when pairing the reads?
Hope your help, thanks.