Previously I thought when the
-g/--max-multihits option in tophat was set to 1, then I acquired the unique mapped reads. However, after careful thinking, I am probably wrong.
Now my idea is: when doing mapping, set the
-g/--max-multihits option to 2 or above 2, and then write a script to eliminate those reads occurring twice or more times. Am I right? Are there any tools or simple approach to obtain unique mapped reads? I appreciate any of your comments and answers. THANKS A LOT!