Transcriptomics gene annotation

Gene annotation adapted from Ensembl's Rattus norvegicus rn6 release 95 GTF. Importantly, MoTrPAC prepended autosomes 'chr' and changed 'MT' to 'chrM'.

Format

A data frame with 32883 rows and 13 variables:

seqname

character, name of the chromosome or scaffold. Chromosome names have the 'chr' prefix.

source

character, name of the program that generated this feature, or the data source (database or project name)

feature

character, feature type name, e.g. Gene, Variation, Similarity

start

integer, start position of the feature, with sequence numbering starting at 1

end

integer, end position of the feature, with sequence numbering starting at 1

score

character, a floating point value

strand

character, defined as + (forward) or - (reverse)

frame

character, one of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on.

gene_id

character, Ensembl gene ID from the 'attribute' field of the GTF

gene_version

character, gene version from the 'attribute' field of the GTF

gene_name

character, gene name from the 'attribute' field of the GTF

gene_source

character, gene source from the 'attribute' field of the GTF

gene_biotype

character, gene biotype from the 'attribute' field of the GTF

Source

https://ftp.ensembl.org/pub/release-95/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.95.gtf.gz

Details

TRNSCRPT feature annotation is only available via download from Google Cloud Storage: https://storage.googleapis.com/motrpac-rat-training-6mo-extdata/feature-annot/TRNSCRPT_FEATURE_ANNOT.rda. You can use MotrpacRatTraining6mo::load_feature_annotation() to download and return this file.