README.md

In vsbuffalo/TxDb.Zmays.Ensembl.AGPv2.17: Annotation package for TranscriptDb object(s)

TxDb.Zmays.Ensembl.AGPv2.17

This TranscriptDb was generated with AGPv2.17 GTF from Ensembl, downloaded with:

wget -O - ftp://ftp.ensemblgenomes.org/pub/plants/release-17/gtf/zea_mays/Zea_mays.AGPv2.17.gtf.gz \
  > inst/extdata/Zea_mays.AGPv2.17.gtf

This GTF was downloaded on 2014-03-08. This version is the last release from Ensemble for AGPv2.

Chromosome length information (inst/extdata/AGPv2.17.lengths.txt) was made with:

wget -O - ftp://ftp.ensemblgenomes.org/pub/plants/release-17/fasta/zea_mays/dna/Zea_mays.AGPv2.17.dna.toplevel.fa.gz \
  | bioawk -c fastx '{print $name"\t"length($seq)"\tFALSE"}' > inst/extdata/Zea_mays.AGPv2.17.lengths.txt

Filtered and Whole Gene Sets

Maizesequence.org (now Gramene) has different annotation than Ensembl, including classification of genes into filtered whole gene sets. Currently, there are 63,331 protein-coding genes in Ensembl's data set (see with length(genes(txdb))). Only a subset of these genes are supported by evidence; others may be pseudogenes or gene fragments (see this description on CoGe for more information). The file inst/extdata/ZmB73_5b_FGS.gff.gz from MaizeSequence.org was processed so as to gather all filtered gene IDs:

gzcat ZmB73_5b_FGS.gff.gz | grep gene | cut -f9 | \
  cut -f1 -d";" | sed 's/ID=//' | sort | uniq > ZmB73_5b_FGS_gene_ids.txt

The file ZmB73_5b_FGS.gff.gz was downloaded on 2014-03-18.

With these filtered IDs, a second TranscriptDb of filtered genes is created: TxDb.Zmays.EnsemblFiltered.AGPv2.17.

Using this Package

Install with:

R CMD INSTALL TxDb.Zmays.Ensembl.AGPv2.17

Then, to use:

library(TxDb.Zmays.Ensembl.AGPv2.17)
txdb <- TxDb.Zmays.Ensembl.AGPv2.17
# or
# txdb <- TxDb.Zmays.EnsemblFiltered.AGPv2.17
exons <- exonsBy(txdb, "gene")

vsbuffalo/TxDb.Zmays.Ensembl.AGPv2.17 documentation built on May 3, 2019, 6:41 p.m.