Extracting positions that are upstream to start site positions

Question

[Jamie Watson]

I am looking at a file and I want to extract only those lines that are upstream relative translation initiation site (TIS). I just want to confirm that upstream here would mean only extracting those lines where position relative to TIS is negative, right? Because a positive value would mean downstream. Also some values relative to TIS is zero. Can I consider those upstream too?

[cpad0112]

You are correct that upstream is represented by - and downstream by +. But I haven't come across zero wrt TSS.

[lieven.sterck]

for clarity: do we consider TIS to be the same as TSS ? To me:

• TIS : Translation Initation site (= protein)
• TSS: Transcription Start Site (= transcript/mRNA)

[cpad0112]

TIS and TSS are different. Your understanding about + and - are correct.