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Extracting positions that are upstream to start site positions

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?

genome
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written by Jamie Watson • Jamie Watson

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

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written by cpad0112 cpad0112

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)
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written by lieven.sterck lieven.sterck

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

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written by cpad0112 cpad0112

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