This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to annotate TTS or TES

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!

chip-seq tes annotation
• 13,174 views • link
written by Lila M Lila M

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

• 0 views • link
written by Lila M Lila M

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.

• 0 views • link
written by Sinji Sinji

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

• 0 views • link
written by Lila M Lila M

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

• 0 views • link
written by Sinji Sinji

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

• 0 views • link
written by Lila M Lila M

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.

• 0 views • link
written by Sinji Sinji

0 answers

No answers yet.

Log in to answer this question.

More posts like this