exampleZv9_annot: Example zebrafish annotation data

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

Annotation data for zebrafish's chromosome 17's interval 26000000-54000000 (Zv9/danRer7 genome), to be used in documentation examples.

Usage

exampleZv9_annot

Format

An object of class GRanges of length 7467.

Details

Data was retreived from ENSEMBL's Biomart server using a query to extract gene, transcripts and exon coordinates. For the record, here it is as URL (long, possibly overflowing).

http://mar2015.archive.ensembl.org/biomart/martview/78d86c1d6b4ef51568ba6d46f7d8b254?VIRTUALSCHEMANAME=default&ATTRIBUTES=drerio_gene_ensembl.default.structure.ensembl_gene_id|drerio_gene_ensembl.default.structure.ensembl_transcript_id|drerio_gene_ensembl.default.structure.start_position|drerio_gene_ensembl.default.structure.end_position|drerio_gene_ensembl.default.structure.transcript_start|drerio_gene_ensembl.default.structure.transcript_end|drerio_gene_ensembl.default.structure.strand|drerio_gene_ensembl.default.structure.chromosome_name|drerio_gene_ensembl.default.structure.external_gene_name|drerio_gene_ensembl.default.structure.gene_biotype|drerio_gene_ensembl.default.structure.exon_chrom_start|drerio_gene_ensembl.default.structure.exon_chrom_end|drerio_gene_ensembl.default.structure.is_constitutive|drerio_gene_ensembl.default.structure.rank&FILTERS=&VISIBLEPANEL=resultspanel

And here it is as XML.

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
  <Dataset name = "drerio_gene_ensembl" interface = "default" >
    <Attribute name = "ensembl_gene_id" />
    <Attribute name = "ensembl_transcript_id" />
    <Attribute name = "start_position" />
    <Attribute name = "end_position" />
    <Attribute name = "transcript_start" />
    <Attribute name = "transcript_end" />
    <Attribute name = "strand" />
    <Attribute name = "chromosome_name" />
    <Attribute name = "external_gene_name" />
    <Attribute name = "gene_biotype" />
    <Attribute name = "exon_chrom_start" />
    <Attribute name = "exon_chrom_end" />
    <Attribute name = "is_constitutive" />
    <Attribute name = "rank" />
  </Dataset>
</Query>

The downloaded file was then transformed as follows.

x <- read.delim("~/Downloads/mart_export.txt", stringsAsFactors = FALSE)
e <- GRanges(paste0("chr", x$Chromosome.Name), IRanges(x$Exon.Chr.Start..bp., x$Exon.Chr.End..bp.), ifelse(x$Strand + 1, "+", "-"))
e$gene_name <- Rle(x$Associated.Gene.Name)
e$transcript_type <- Rle(x$Gene.type)
e$type <- "exon"
e$type <- Rle(e$type)

e <- GRanges(paste0("chr", x$Chromosome.Name), IRanges(x$Exon.Chr.Start..bp., x$Exon.Chr.End..bp.), ifelse(x$Strand + 1, "+", "-"))
e$gene_name <- Rle(x$Associated.Gene.Name)
e$transcript_type <- Rle(x$Gene.type)
e$type <- "exon"
e$type <- Rle(e$type)
e <- sort(unique(e))

g <- GRanges( paste0("chr", x$Chromosome.Name)
            , IRanges(x$Gene.Start..bp., x$Gene.End..bp.)
            , ifelse( x$Strand + 1, "+", "-"))
            
g$gene_name <- Rle(x$Associated.Gene.Name)
g$transcript_type <- Rle(x$Gene.type)
g$type <- "gene"
g$type <- Rle(g$type)
g <- sort(unique(g))

t <- GRanges( paste0("chr", x$Chromosome.Name)
            , IRanges(x$Transcript.Start..bp., x$Transcript.End..bp.)
            , ifelse( x$Strand + 1, "+", "-"))
            
t$gene_name <- Rle(x$Associated.Gene.Name)
t$transcript_type <- Rle(x$Gene.type)
t$type <- "transcript"
t$type <- Rle(t$type)
t <- sort(unique(t))

gff <- sort(c(g, t, e))
gff <- gff[seqnames(gff) == "chr17"]
gff <- gff[start(gff) > 26000000 & end(gff) < 54000000]
seqlevels(gff) <- seqlevelsInUse(gff)

save(gff, "data/exampleZv9_annot.RData", compress = "xz")

Author(s)

Prepared by Charles Plessy [e-mail] using archive ENSEMBL data.

References

http://mar2015.archive.ensembl.org/biomart/

CAGEr documentation built on Jan. 17, 2021, 2 a.m.