This respository contains R scripts and a YAML config file to build
- a custom
BSgenomeR library, and - a custom
TxDbR library
based on the Ensembl GRCh38 genome assembly/annotation and the GenBank U13369.1 canonical rDNA sequence/annotation.
The following R libraries are required.
-
From CRAN:
devtoolsoptparsetidyverseyaml
-
From Bioconductor:
BSgenomeGenomicFeatures
You can install CRAN packages with e.g. install.packages("tidyverse");, and packages from Bioconductor with e.g. source("http://www.bioconductor.org/biocLite.R"); biocLite("BSgenome").
Note that this needs to be done only once. Provided building/installing was successful, the packages will be available within the R environment as libraries.
-
Clone this respository
git clone https://github.com/mevers/build_custom_BSgenome_TxDb -
Change to folder that constains the scripts and config file.
cd build_custom_BSgenome_TxDb -
To build the R packages, there are two options.
-
make_packages.shis a convenience bash script that builds both theBSgenomeandTxDbR packages. Run the script with:sh make_packages.shNote that this will only work on Linux/Unix systems.
-
You can build the R packages separately;
make_BSgenome_package.Randmake_TxDb_package.Rare two R command-line scripts that build theBSgenomeandTxDbpackages, respectively. Run the scripts with:Rscript make_BSgenome_package.R -i config.yamland
Rscript make_TxDb_package.R -i config.yamlOn a Windows systems, you might have to call
Rscriptwith its full path at the Windows command prompt, e.g.C:\R-3.4.3\bin\x64\Rscript.exe(depending on where R is installed).
-
-
After the packages have been successfully build you should see two files
BSgenome.Hsapiens.mevers.hs1_1.0.0.tar.gzandTxDb.Hsapiens.mevers.hs1_1.0.0.tar.gz. Install both packages in R in the usual way, e.g.install.packages("BSgenome.Hsapiens.mevers.hs1_1.0.0.tar.gz", repos = NULL, type = "source"); install.packages("TxDb.Hsapiens.mevers.hs1_1.0.0.tar.gz", repos = NULL, type = "source");
Both the BSgenome and TxDb libraries can now be loaded within R.
library("BSgenome.Hsapiens.mevers.hs1");
library("TxDb.Hsapiens.mevers.hs1");
Get a general genome sequence summary:
BSgenome.Hsapiens.mevers.hs1;
#Human genome:
## organism: Homo sapiens (Human)
## provider: Ensembl+NCBI
## provider version: hs1
## release date: Mar. 2018
## release name: Human masked chromosome plus MT plus rDNA sequences
## 26 sequences:
## chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8
## chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16
## chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY
## chrM U13369.1
## (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
## to access a given sequence)
Extract lengths and features of individual chromosome sequences:
seqinfo(BSgenome.Hsapiens.mevers.hs1);
#Seqinfo object with 26 sequences (2 circular) from hs1 genome:
# seqnames seqlengths isCircular genome
# chr1 248956422 FALSE hs1
# chr2 242193529 FALSE hs1
# chr3 198295559 FALSE hs1
# chr4 190214555 FALSE hs1
# chr5 181538259 FALSE hs1
# ... ... ... ...
# chr22 50818468 FALSE hs1
# chrX 156040895 FALSE hs1
# chrY 57227415 FALSE hs1
# chrM 16569 TRUE hs1
# U13369.1 42999 TRUE hs1
Extract all U13369.1 transcripts:
txdb <- TxDb.Hsapiens.mevers.hs1;
gr <- transcripts(txdb, columns = c("gene_id", "tx_id", "tx_name"));
gr[seqnames(gr) == "U13369.1"];
#GRanges object with 1 range and 3 metadata columns:
# seqnames ranges strand | gene_id tx_id tx_name
# <Rle> <IRanges> <Rle> | <CharacterList> <integer> <character>
# [1] U13369.1 [1, 13314] + | rDNA 199168 pre-rRNA
# -------
# seqinfo: 26 sequences (2 circular) from an unspecified genome; no seqlengths
Or extract all U13369.1 "exons":
gr <- exons(txdb, columns = c("exon_id", "exon_name", "tx_name", "gene_id"));
gr[seqnames(gr) == "U13369.1"];
#GRanges object with 7 ranges and 4 metadata columns:
# seqnames ranges strand | exon_id exon_name tx_name
# <Rle> <IRanges> <Rle> | <integer> <character> <CharacterList>
# [1] U13369.1 [ 1, 3656] + | 680542 5'ETS pre-rRNA
# [2] U13369.1 [ 3657, 5527] + | 680543 18S-rRNA pre-rRNA
# [3] U13369.1 [ 5528, 6622] + | 680544 ITS1 pre-rRNA
# [4] U13369.1 [ 6623, 6779] + | 680545 5.8S-rRNA pre-rRNA
# [5] U13369.1 [ 6780, 7934] + | 680546 ITS2 pre-rRNA
# [6] U13369.1 [ 7935, 12969] + | 680547 28S-rRNA pre-rRNA
# [7] U13369.1 [12970, 13314] + | 680548 3'ETS pre-rRNA
# gene_id
# <CharacterList>
# [1] rDNA
# [2] rDNA
# [3] rDNA
# [4] rDNA
# [5] rDNA
# [6] rDNA
# [7] rDNA
# -------
# seqinfo: 26 sequences (2 circular) from an unspecified genome; no seqlengths
For more details, see e.g.
- Efficient genome searching with Biostrings and the BSgenome data packages
- An overview of the Biostrings/BSgenome framework
- Making and utilizing TxDb Objects
Ensembl data are based on the
- GRCh38 genome assembly, release 89
- the GRCh38.89 GTF annotation file.
In case of questions please contact Maurits Evers.
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