Question: How to annotate TTS or TES
1
gravatar for Lila M
9 weeks ago by
Lila M 230
UK
Lila M 230 wrote:

Hi everybody,

I'm performing some gene profiles from my ChiP seq experiment. To do that, I've used homer or ChipSeeker for the annotation. I am deeply interested in get (not only) the Transcription Start Sites (TSS) and Transcription End Site (TES) for each gene, to perform downstream analysis. Does any anybody can suggest any tool or package for get this data?

Thank you!

tes chip-seq annotation • 152 views
ADD COMMENTlink written 9 weeks ago by Lila M 230

If you got human or mouse data, you could download the FANTOM5 (http://fantom.gsc.riken.jp/data/) annotated promoters and use an intersecting tool to annotate your start sites with that.

ADD REPLYlink written 9 weeks ago by Floris Brenk770

I have the TSS what I need is the TTS.could be ok if I do : TSS+geneLength = TTS?

ADD REPLYlink written 9 weeks ago by Lila M 230

Couldn't you just use the gene names as input into the UCSC browser and make a BED file of them? That would include the TSS and TES.

ADD REPLYlink written 9 weeks ago by Sinji2.1k

Also a list of more than 20000000 genes? I can't upload one by one.. can I do all at the same time?

ADD REPLYlink written 9 weeks ago by Lila M 230
1

What kind of genome are you working with where you have 20 million genes?

ADD REPLYlink written 9 weeks ago by Sinji2.1k

It is an example, because If I have 2000 genes, I can't look for the TTS manualy in USCS, please, could you explain your aproach better?

Thank

ADD REPLYlink written 9 weeks ago by Lila M 230

Essentially what I am suggesting is you take the gene name for all 2000 of your genes. You "paste" the list into UCSC table browser for your genome, and then you download the file in .bed format. That will give you a your TSS in Column 2 and your TES in Column 3.

ADD REPLYlink written 9 weeks ago by Sinji2.1k
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