Hi everyone,

I am new to TxDb objects and stuff like that, so please excuse my questions. I downloaded both base features and repeat feature data sets from Aedes aegypti from Vectorbase (https://www.vectorbase.org/downloads?field_organism_taxonomy_tid=372&field_download_file_type_tid=All&field_download_file_format_tid=474&field_status_value=Current).
I would then like to create a TxDb object and from that a annoGR object to use this with annotationPeakInBatch from ChipPeakAnno but I fail to do so with the repeat feature data set. The created object is just empty. However, with the base feature data set (and same bit of code) it works quite well.

Does anyone has any suggestions for me how to solve that?

Thanks a ton,

Rebecca

>Aaegypti_TxDb_rep=makeTxDbFromGFF("Aedes-aegypti-Liverpool_REPEATFEATURES_AaegL3.gff3",
format="auto", dataSource = "EnsembleMetazoa",
organism = "Aedes aegypti")

Import
genomic features from the file as a GRanges object ... OK

Prepare
the 'metadata' data frame ... OK

Make
the TxDb object ... OK

Warnmeldung:

In
.local(con, format, text, ...) : gff-version directive indicates version is   3, not 3

>Aaegypti_TxDb_rep
TxDb
object:
#Db type: TxDb
#Supporting package: GenomicFeatures
#Data source: EnsembleMetazoa
#Organism: Aedes aegypti
#Taxonomy ID: 7159
#miRBase build ID: NA
#Genome: NA
#transcript_nrow: 0
#exon_nrow: 0
#cds_nrow: 0
#Db created by: GenomicFeatures package from Bioconductor
#Creation time: 2015-11-19 13:57:31 +0100 (Thu, 19 Nov 2015)
#GenomicFeatures version at creation time: 1.22.4
#RSQLite version at creation time: 1.0.0
#DBSCHEMAVERSION: 1.1

> keytypes(Aaegypti_TxDb_rep)
[1]
"CDSID"    "CDSNAME"  "EXONID"
"EXONNAME" "GENEID"   "TXID"  
"TXNAME"  

> columns(Aaegypti_TxDb_rep)
[1]
"CDSCHROM"   "CDSEND"     "CDSID"   
"CDSNAME"    "CDSSTART"   "CDSSTRAND"
"EXONCHROM"  "EXONEND"    "EXONID"  
"EXONNAME"  

[11]
"EXONRANK"   "EXONSTART"  "EXONSTRAND"
"GENEID"     "TXCHROM"    "TXEND"   
"TXID"       "TXNAME"     "TXSTART" 
"TXSTRAND"  

[21]
"TXTYPE" 

 >sessionInfo()

R
version 3.2.2 (2015-08-14)

Platform:
x86_64-pc-linux-gnu (64-bit)

Running
under: Ubuntu 14.04.3 LTS

locale:

 [1]
LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C            
LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8  
LC_MONETARY=de_DE.UTF-8   

 [6]
LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C    
           LC_ADDRESS=C               LC_TELEPHONE=C            

[11]
LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached
base packages:

[1]
stats     graphics  grDevices utils     datasets  methods   base     

other
attached packages:

[1]
BiocInstaller_1.20.0

loaded
via a namespace (and not attached):

[1]
tools_3.2.2

>source("http://bioconductor.org/biocLite.R")

Bioconductor
version 3.2 (BiocInstaller 1.20.0), ?biocLite for help

Hi Rebecca,

There are 2 GFF3 files available at the URL you provided:

1. Aedes-aegypti-Liverpool_BASEFEATURES_AaegL3.3.gff3.gz: Liverpool strain AaegL3.3 geneset in GFF3 format.
2. Aedes-aegypti-Liverpool_REPEATFEATURES_AaegL3.gff3.gz: Liverpool strain AaegL3 repeat features (RepeatMasker, Dust, TRF) in GFF3 format.

You picked up the 2nd one, which doesn't seem to contain gene or transcript information. You'll probably have better luck with the 1st one.

Cheers,

H.