How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
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@c315f3e7
Last seen 3 months ago
Germany

I have an issue using the functionality of the R package customProDB to download annotation data from Ensembl as described in the documentation (2.2 ENSEMBL annotation from BIOMART). To check for yourself use browseVignettes("customProDB"). I saw multiple other users had the issue in the past like here: GenomicFeatures makeTranscriptDbFromBiomart 'chrominfo' data frame ... FAILED! . However, those threads weren't useful to resolve my issue.

The issue is that it fails to download the 'chrominfo' data frame. A subsequent function of customProDB however needs that data.

How do I get the chrominfo?

# install necessary packages
# if (!requireNamespace("BiocManager", quietly = TRUE))
#   install.packages("BiocManager")
# 
# BiocManager::install("customProDB")

library(customProDB)
library(seqinr)
library(glue)
library(rtracklayer)

# open documentation in browser
# browseVignettes("customProDB")

# specify annotation data from ENSEMBL
ensembl <- useMart(
  "ENSEMBL_MART_ENSEMBL", 
  dataset="hsapiens_gene_ensembl",
  host="dec2021.archive.ensembl.org",
  path="/biomart/martservice", 
  archive=FALSE
)

# where to save the downloaded data
annotation_path <- "~/Documents/ncHLAII_immunopeptidomics/ensembl"
dir.create(annotation_path)

# download and save the annotation data
PrepareAnnotationEnsembl(
  mart=ensembl, 
  annotation_path=annotation_path, 
  splice_matrix=FALSE, 
  dbsnp=NULL, 
  COSMIC=FALSE
)

Output from Console:

Prepare gene/transcript/protein id mapping information (ids.RData) ...  done
Build TranscriptDB object (txdb.sqlite) ... 
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... 
biomaRt customProDB • 150 views
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