parse_TxDb {InPAS} | R Documentation |
Extract gene models from a TxDb object and annotate last 3' UTR exons and the last CDSs
parse_TxDb(TxDb = NULL, edb = NULL, removeScaffolds = FALSE)
TxDb |
An object of GenomicFeatures::TxDb |
edb |
An object of ensembldb::EnsDb |
removeScaffolds |
A logical(1) vector, whether the scaffolds should be removed from the genome If you use a TxDb containing alternative scaffolds, you'd better to remove the scaffolds. |
A good practice is to perform read alignment using a reference genome from Ensembl/GenCode including only the primary assembly and build a TxDb using the GTF/GFF files downloaded from the same source as the reference genome, such as BioMart/Ensembl/GenCode. For instruction, see Vignette of the GenomicFeatures. The UCSC reference genomes and their annotation can be very cumbersome.
A GenomicRanges::GRanges object for gene models
Haibo Liu
library("EnsDb.Hsapiens.v86") library("GenomicFeatures") samplefile <- system.file("extdata", "hg19_knownGene_sample.sqlite", package = "GenomicFeatures") TxDb <- loadDb(samplefile) edb <- EnsDb.Hsapiens.v86 parsed_Txdb <- parse_TxDb(TxDb, edb, removeScaffolds = TRUE)