Recommended Tools For 3'UTR APA Detection From Rna-Seq Data?

Question

[gandrescabrera]

{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.

Answer 1

[i.sudbery]

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.

[gandrescabrera]

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

[gandrescabrera]

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

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

[i.sudbery]

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

Answer 2

[gandrescabrera]

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

Cheers

[GenoMax]

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