How to choose one TSS for a gene

Question

[GG]

Hello,

I need to get the transcription start site for several genes. However, the ncbiRefSeq file from the UCSC browser gives more than one TSS value for one gene (because some genes have several transcripts). If I need to choose one TSS value, how should I do this? How should I identify the more "common" TSS for a gene? Or if there's another approach to choose one TSS value, please comment below!

Thank you very much!

[Papyrus]

I haven got to using it yet, but maybe you could use the NCBI-EMBL MANE track. It provides a unique representative transcript making use of both NCBI + ensembl knowledge (it's a work in progress so maybe all genes haven't been covered yet).

[GG]

I see! I checked it out:) thank you so much for your suggestion!!

[Alex Reynolds]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6613478/

[GG]

Thank you for the reference!

[Alex Reynolds]

Does TSS = first exon?

Answer 1

[heskett]

There is no one best way to choose a TSS, since they may be different in each tissue. you can use a heuristic like the middle one, or try to get tissue specific information from GTEX or something similar. I guess it depends on what you are using the TSS sites for?

[GG]

That makes sense! Thank you for the suggestions :)