exampleZv9_annot: Example zebrafish annotation data

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

Example zebrafish annotation data

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/

charles-plessy/CAGEr documentation built on Oct. 27, 2024, 10:11 p.m.