Question: Best current ways to find TSS please (even cell dependent ones)?
0
gravatar for Aurelie MLB
22 months ago by
Aurelie MLB320
United Kingdom
Aurelie MLB320 wrote:

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 • 588 views
ADD COMMENTlink written 22 months ago by Aurelie MLB320

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/

ADD REPLYlink written 22 months ago by Santosh Anand4.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2080 users visited in the last hour