Best current ways to find TSS please (even cell dependent ones)?
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4.4 years ago
Aurelie MLB ▴ 360

Hello,

I am trying to map the TSS of genes in the whole genome. I did look for what people were proposing already but the last posts on this subject are quite old. I was wondering if the current view would be different. Examples of what I have seen so far are:

But what about CAGE data from FANTOM5? Doesn't it provide TSS as well by a more data driven method? There is a lot of complexe data in FANTOM5. I never used it. Is there some pitfall I should avoid please? How do I get a nice file with measured TSS per transcripts ? (is it possible?)

What would be the best method according to you? Given that of course my experiment has been done in a specific cell... Should I go as far as getting TSS for that cell type? How would I do this?

A lot of questions sorry! I am starting on this. But I thought it might be useful to others than me given all the new CRISPRa/i screens coming up.

Many thanks Aurelie

genome • 958 views
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You might be also interested in EPD, which is curated promoter database. http://epd.vital-it.ch/index.php

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531148/

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