Dear all,
What software do you use to detect alternative polyadenylation from standard short-read RNA-seq?
Thanks, Gregor
Found this review for now:
"A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data"
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? :)
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
Nice! Will check it out, didn't see this one, the docs also look to be there, thanks again
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...
Another one I found is QAPA, https://github.com/morrislab/qapa
This one seems updated and recent:
APAlyzer: https://www.bioconductor.org/packages/devel/bioc/vignettes/APAlyzer/inst/doc/APAlyzer.html
Log in to answer this question.
