Finding unusual genomes with AnnotationHub
1
@theokirkland3-20611
Last seen 9 months ago
United States
I am am trying to load the genome for a fungus named Coccidioides immitis using AnnotationHub. The data is not in the UCSC database. I know the data is in FungiDB and the NCBI ftp site, which are listed as data sources. Any suggestions?
annotation
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@james-w-macdonald-5106
Last seen 2 hours ago
United States
What exactly do you mean by 'genome'? The actual sequences for each chromosome? The gene locations?
If the latter, consider:
> library(AnnotationHub)
> hub <- AnnotationHub()
> z <- query(hub, c("coccidioides immitis", "gff"))
> z
AnnotationHub with 4 records
# snapshotDate(): 2019-04-23
# $dataprovider: FungiDB
# $species: Coccidioides immitis
# $rdataclass: GRanges, OrgDb
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH65067"]]'
title
AH65067 | Coccidioides immitis RS genome wide annotations
AH65102 | Coccidioides immitis H538.4 genome wide annotations
AH65332 | Coccidioides immitis RS transcript information
AH65367 | Coccidioides immitis H538.4 transcript information
> CI <- hub[["AH65367"]]
> library(GenomicFeatures)
> CITX <- makeTxDbFromGRanges(CI)
> CITX
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Genome: FungiDB-39_CimmitisH538-4
# transcript_nrow: 10779
# exon_nrow: 34394
# cds_nrow: 33111
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2019-04-24 12:17:05 -0700 (Wed, 24 Apr 2019)
# GenomicFeatures version at creation time: 1.35.9
# RSQLite version at creation time: 2.1.1
# DBSCHEMAVERSION: 1.2
> genes(CITX)
GRanges object with 10724 ranges and 1 metadata column:
seqnames ranges strand | gene_id
<Rle> <IRanges> <Rle> | <character>
CIHG_00001 DS016981 23315-24814 - | CIHG_00001
CIHG_00002 DS016981 25495-26017 - | CIHG_00002
CIHG_00003 DS016981 26612-27769 + | CIHG_00003
CIHG_00004 DS016981 28041-28790 - | CIHG_00004
CIHG_00005 DS016981 30086-32910 - | CIHG_00005
... ... ... ... . ...
CIHG_11112 DS017050 56849-56930 + | CIHG_11112
CIHG_11113 DS017057 33332-33404 + | CIHG_11113
CIHG_11114 DS017059 28091-28181 - | CIHG_11114
CIHG_11115 DS017074 13684-13767 + | CIHG_11115
CIHG_11116 DS017239 3077-3148 + | CIHG_11116
-------
seqinfo: 229 sequences from FungiDB-39_CimmitisH538-4 genome; no seqlengths
If you mean the actual sequences, then there is a vignette .
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