Could you clarify TES? You say TSS at one point but TES in other locations, including the title.

Best to avoid too much jargon, or at least define it up front. TES = Transcription End Site (as opposed to TSS, Transcription Start Site), and sometimes referred to as TTS = Transcription Termination Site. K36 = H3K36me3, pol2 = RNA pol II. Also, "best" is a hairy term, dependent on the question you're asking (which isn't specified in the question above). "Best" is defined relative to some purpose. For TSS, if a gene has many choices of TSS, you chose the "best" one by taking the one with the highest pol II signal, as presumably this would indicate which TSS is being used by the locus, but this could depend on which pol II antibody was used for polymerase detection. For TES, if many choices are available, "best" might be defined as H3K36me3 signal 5' of TES, but less signal 3' of TES. Your question might be rephrased: is there a chromatin mark or signature that defines Transcription Termination Sites? Or does anyone have a method for correlating or scoring Transcription Termination Sites with active marks of transcription, such as H3K36me3?