Question: Best current ways to find TSS please (even cell dependent ones)?
gravatar for Aurelie MLB
2.8 years ago by
Aurelie MLB340
United Kingdom
Aurelie MLB340 wrote:


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 • 749 views
ADD COMMENTlink written 2.8 years ago by Aurelie MLB340

You might be also interested in EPD, which is curated promoter database.


ADD REPLYlink written 2.8 years ago by Santosh Anand5.1k
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