How to find genomic position

Question

[suxxa]

Hi! I'm wondering how to retrieve, from a given circRNA ( e.g. hsa_circRNA_405987), the genomic position in human genome 19 coordinates ( e.g. 121765368) using R.

Do you have any ideas about it?

Thanks!

[suxxa]

Maybe I should do a preliminary step to find from circRNA to transcript and then from transcript to gene SYMBOL? Something like that?

[manaswwm]

If you can go from circRNA to transcript (I am sure there will be a way to do this, I am unaware of this though), then you could use the REST-API of Ensembl to get the transcript specific coordinates. For example for the transcript - ENST00000496384, you could do something like this (code copied from Ensembl REST-API page):

library(httr)
library(jsonlite)
library(xml2)

server <- "https://grch37.rest.ensembl.org"
ext <- "/lookup/id/ENST00000496384?expand=1"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))

The "target URL" looks something like this - https://rest.ensembl.org/lookup/id/ENST00000496384?expand=1;content-type=application/json. For multiple transcripts, you could consider using POST method instead of GET (refer to the code) - https://grch37.rest.ensembl.org/documentation/info/lookup_post - here you can ask for information on multiple ids in a single request.