Question: TxDb basic question
0
gravatar for Brian Smith
10 months ago by
Brian Smith120
United States
Brian Smith120 wrote:

Hi,

I was exploring the rhesus macaque package:

> TxDb.Mmulatta.UCSC.rheMac8.refGene
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC rheMac8 refGene
# Organism: Macaca mulatta
# Taxonomy ID: 9544
# miRBase build ID: NA
# Genome: NA
# transcript_nrow: 6378
# exon_nrow: 46356
# cds_nrow: 43281
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2017-10-02 12:20:15 -0400 (Mon, 02 Oct 2017)
# GenomicFeatures version at creation time: 1.29.11
# RSQLite version at creation time: 2.0
# DBSCHEMAVERSION: 1.1
# Resource URL: http://genome.ucsc.edu/cgi-bin/hgTables

 

Does "# transcript_nrow: 6378" mean that there is information for only, at most, 6378 genes in this package. Sorry, not familiar with this organism, but doesn't 6378 genes seem a bit on the small size considering it is for the entire genome?

Or have I mis-understood something?

many thanks!

ADD COMMENTlink modified 10 months ago by daniel.vantwisk50 • written 10 months ago by Brian Smith120
Answer: TxDb basic question
0
gravatar for daniel.vantwisk
10 months ago by
daniel.vantwisk50 wrote:

It appears that the transcript_nrow is correct.  This link points us to the RefSeq Genes table from UCSC:

https://genome.ucsc.edu/cgi-bin/hgTables?db=rheMac8&hgta_group=genes&hgta_track=refGene&hgta_table=refGene&hgta_doSchema=describe+table+schema

Given each row in the table accounts for a transcript, the 6484 transcripts is a very close to the 6378 transcripts in question.  The remaining hundred-or-so transcripts may have been excluded from the TxDb.Mmulatta.UCSC.rheMac8.refGene due to not meeting various constraints such as a cds not being a multiple of three.

ADD COMMENTlink modified 10 months ago • written 10 months ago by daniel.vantwisk50
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