I have BAM files which were run with tophat and --fusion-search --fusion-min-dist 1000000 --fusion-read-mismatches 2 --fusion-multireads 1 --fusion-multipairs 1 --fusion-anchor-length 10 -p 14.

I have 2 questions:

1. How can I create new BAM files from the current ones but with no fusion reads?

2. If I remove the fusion reads from the current BAM files would the resulting BAM files be exactly the same as if it was created without running tophat with --fusion-search?