Description

Transcript ranges and strand information for a particular reference genome.

Usage

Format

A data.table which contains transcript range and strand information for a particular reference genome. colnames are chrom, start, end, strand, Ensembl.gene.ID, gene.symbol. It uses one-based coordinates.

An object of class data.table (inherits from data.frame) with 19083 rows and 6 columns.

An object of class data.table (inherits from data.frame) with 19096 rows and 6 columns.

An object of class data.table (inherits from data.frame) with 20325 rows and 6 columns.

Details

This information is needed to generate catalogs that depend on transcriptional strand information, for example catalogs of class SBS192Catalog.

trans.ranges.GRCh37: Human GRCh37.

trans.ranges.GRCh38: Human GRCh38.

trans.ranges.GRCm38: Mouse GRCm38.

For these two tables, only genes that are associated with a CCDS ID are kept for transcriptional strand bias analysis.

This information is needed for StrelkaSBSVCFFilesToCatalog,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf, MutectVCFFilesToCatalog,
MutectVCFFilesToCatalogAndPlotToPdf, VCFsToSBSCatalogs and VCFsToDBSCatalogs.

Source

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/GRCh37_mapping/gencode.v30lift37.annotation.gff3.gz

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gff3.gz

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M21/gencode.vM21.annotation.gff3.gz

Examples