Is there a way to add a transcript to EnsDb.Hsapiens.v86?
Entering edit mode
3 months ago
Daniel ▴ 30


I am trying to use ensembldb's transcriptToGenome function, using EnsDb.Hsapiens.v86 as the db. My code below is:

library(ensembldb) library(EnsDb.Hsapiens.v86)

edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "8") rng_tx <- IRanges(start = c(10), width = c(42), names = c("ENST00000657517"))

rng_gnm <- transcriptToGenome(rng_tx, edbx) rng_gnm

I get

Warning message: In transcriptToGenome(rng_tx, edbx) : 1 transcript(s) could either not be found in the database or the specified range is outside the transcript's sequence

From ensembl, I know that this range is within the transcripts sequence, so I believe it is just not in EnsDb. Is there a way I can "add" this to the database, or create a new db object in R?

Thank you!

ensembldb GenomicFeatures R Bioconducter EnsDb.Hsapiens.v86 • 366 views
Entering edit mode
3 months ago
Daniel ▴ 30

If anyone needs this, figured it out. Instead of adding data to the database, you just need to pull the newest release and save it (takes a while the first time). R code here (for ensembl release 109 and human genome):

ah <- AnnotationHub() query(ah, "EnsDb")

ahDb <- query(ah, pattern = c("Homo Sapiens", "EnsDb", 109)) ahEdb <- ahDb[[1]]


Login before adding your answer.

Traffic: 1143 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6