You had to use various tools, cut the transport streams, join them back and convert them to the desired format.
This lightweight application is completely free and everyone is encouraged to use it.
The main features of the IFrames Transport Stream Cutter are its fast speed, the small index files, and the ability to scroll through the video to determine cutting limits. Video fades, blank and split will not be a problem anymore.
The IFrames Transport Stream Cutter has not been developed anymore since 2008, although its developer had in mind improving the application with more command line options, multistream TS capability and better auto-split cuts for low light video content.
An issue you may encounter in IFrames Transport Stream Cutter is some HD video streams only displaying the left half of the picture, even if the entire video frame eventually appears in the output file.
The last version of the IFrames Transport Stream Cutter was 184.108.40.206 and it required a .Net 2.x Framework runtime. It was improved with a cut button split in three parts.
The central part is for cutting without saving that point as a user defined cut point. The left part will add the frame to the left of the cut point, while clicking the right portion will use the frame to the right of the cut point as a user defined cut point.
The developer of the IFrames Transport Stream Cutter had the idea of creating this application after noticing how difficult cutting TS into pieces was.