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Uh, "encode .ts file", do you mean use whatever as input and produce a TS as output, or use a TS as input and produce whatever as output?
Trust me, you don't want to produce transport streams, it's a format designed for heavy fault tolerance in digital broadcast systems, so it doesn't matter if the signal drops out for several seconds at a time. This means it has a huge overhead; if you mux the same elementary streams as TS and as MP4 you will see that the TS file is significantly larger.
If you want to use a TS as a source, what I prefer is using a program such as ProjectX (there's also another one I can't remember the name of) to demux the transport stream into elementary streams which can then be handled by regular tools, eg. parse an M2V file with DGIndex and then source it into Avisynth with DGDecode.
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