Question: Identify transcription start site using RNA-seq data
gravatar for I0110
14 months ago by
United States
I0110120 wrote:

I am wondering if there is a tool available to identify eukaryotic transcription start site using regular RNA-seq data? I know people use cap-seq to select 5' cap of mRNA and sequence them. However, there are a lot more RNA-seq data available. It would be interesting if we can try using RNA-seq data to identify transcription start site. Thanks!

rna-seq • 631 views
ADD COMMENTlink modified 14 months ago by ababaian20 • written 14 months ago by I0110120
gravatar for ababaian
14 months ago by
ababaian20 wrote:

I've spent a lot of time working on this problem but in the subset of TSS in Transposable Elements. You can do the trivial analysis such as assembly + look at the 5' end of Exon 1 but I was interested in a lot of the areas in which the assemblies didn't work so well (TSSs in repeats). In general RNA-seq + assembly doesn't do so hot for finding true 5' ends.

I put together a little bit of software for this called LIONS. It does what I want pretty well but to be honest, I think a similar application of ANNs to all transcriptome data can vastly improve TSS calling, I just never had the need to generalize this solution for all TSSs. Might be a starting place for you if you're looking to go after this problem in a serious capacity.

ADD COMMENTlink written 14 months ago by ababaian20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1220 users visited in the last hour