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How to find genomic position

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!

r gene circrna

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

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.

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