Recommended Tools For 3'UTR APA Detection From Rna-Seq Data?
2
0
Entering edit mode
3.7 years ago

{tl;dr}looking for useful tools for 3'UTR dynamic expression detection at transcriptomic data

Hi,

I have been working with RNAseq data, looking for different events like alternative splicing. Now I have a question about the 3'UTR shortening/lengthening between 2 conditions on humans.

I have been using R language, but also trying new tools.

By now I have been using "roar" R package, which can be found at Bioconductor repository. It's promising, but I might need to overlift the inbuilt GTF which is hg19, to hg38 genome (my reference genome).

roar's bioconductor: https://bioconductor.org/packages/release/bioc/html/roar.html

roar's paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1254-8

Im also trying a sliding window (R) from terminal exons, but its heuristic and I have no experience at sliding windows, so I suppose it will take me some time until I improve it.

Some info about it (not my blog): http://coleoguy.blogspot.com.uy/2014/04/sliding-window-analysis.html

I think this may work, but I also think you might know something useful, or even better, for this job,

Thanks in advance!

G.

RNA-Seq R Polyadenylation UTR tools • 1.4k views
ADD COMMENT
1
Entering edit mode
3.7 years ago

You might like to try DaPars: http://lilab.research.bcm.edu/dldcc-web/lilab/zheng/DaPars_Documentation/html/DaPars.html

Its the tool i've used the most, although its never led to any significant discovery for us. I'd be interested in how you get on cf roar.

ADD COMMENT
1
Entering edit mode

Hey I had found this tool called "APATrap" which seems to work pretty good, and has comparations with DaParse and ChangePoint. The package "roar" was good for a first impression, but its still under development, I guess it gave me little information about the most expressed APAs, but little information or bad signals about those with poor expression. I even spotted some APAs that were not considered. But this is pretty normal since i did it using a Overlifted hg19 to hg38 GTF, from APADB_2, which may lead to incomplete outputs, limiting the insights.

I give you a link for APAtrap information: https://omictools.com/apatrap-tool paper: https://www.ncbi.nlm.nih.gov/pubmed/29360928

ADD REPLY
0
Entering edit mode

Hello, and thanks for your recommendation. Btw, what did you mean with "cf"?

Lets stay in touch, i'm glad to collaborate.

ADD REPLY
0
Entering edit mode

Sorry, cf means "compared with" https://en.wikipedia.org/wiki/Cf.

ADD REPLY
0
Entering edit mode
5 months ago

I have had good results with APATrap, anyone tried it already?

Cheers

ADD COMMENT
0
Entering edit mode

If you are recommending a tool then please provide a link for the software repo/website.

ADD REPLY

Login before adding your answer.

Traffic: 2444 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6