Alternative polyadenylation detection from short-read RNA-seq, software suggestions

Question

[Gregor Rot]

Dear all,

What software do you use to detect alternative polyadenylation from standard short-read RNA-seq?

Thanks, Gregor

Answer 1

[Gregor Rot]

Found this review for now:

"A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data"

https://academic.oup.com/bib/article/21/4/1261/5522019

Answer 2

[i.sudbery]

We have successfully used DaPars before. But we've no real reason to suspect its the best, but it found at least some things we believed.

[Gregor Rot]

Thanks! Looking at the DaPars repo https://github.com/ZhengXia/DaPars, the docs link are broken and the project seems not to be so well maintained. Do you remember when you used this software last? :)

[i.sudbery]

We last used it earlier this year, but that doesn't mean we installed it then.

Looking around, I see their appears to be a DaPars2, which appears to be more actively maintained. https://github.com/3UTR/DaPars2

[Gregor Rot]

Nice! Will check it out, didn't see this one, the docs also look to be there, thanks again

[Gregor Rot]

Uh still, python2.7 and so on, struggling with setting it up, is there really no more up-to-date package to get some RNA-seq analyzed for APA? I wonder...

[i.sudbery]

I'm sure there are lots more, thats just the one I've used.

Answer 3

[Gregor Rot]

Another one I found is QAPA, https://github.com/morrislab/qapa

Answer 4

[Gregor Rot]

This one seems updated and recent:

APAlyzer: https://www.bioconductor.org/packages/devel/bioc/vignettes/APAlyzer/inst/doc/APAlyzer.html