Hi Song, The message about CDS availability refers just to the ranges needed to populate the CDS tables. However, if you are like a lot of people you will only be asking questions about transcripts and exons, and in that case, I bet that this will not affect you. Marc On 12/13/2010 07:00 AM, Song Li wrote: > Hi Herv? , > > Thank you for the reply. > > I am little worried about the warning message that "CDS" is not > available. However, it does not seem to be a crucial factor to > consider at this moment. > > Best, > Song > > 2010/12/11 Hervé Pagès <hpages at="" fhcrc.org="">: > >> Hi Song, >> >> On 12/10/2010 11:16 AM, Song Li wrote: >> >>> Hi, All, >>> >>> I want to thank you for the incredible package which greatly >>> simplifies our analysis for RNA-seq. >>> >>> However, I am working with Arabidopsis RNA-seq data, however, it seems >>> that I have to build a transcriptDb object by myself. Is there a >>> function that reads GTF file and make transcriptDB object? >>> >> No we don't have this yet but we might add it in the future. >> In the mean time you can build a TranscriptDb object for >> Arabidopsis by using the alyrata_eg_gene dataset from the >> plant_mart_7 Mart: >> >> >>> library(GenomicFeatures) >>> >> >>> txdb <- makeTranscriptDbFromBiomart("plant_mart_7", "alyrata_eg_gene") >>> >> Download and preprocess the 'transcripts' data frame ... OK >> Download and preprocess the 'splicings' data frame ... OK >> Download and preprocess the 'genes' data frame ... OK >> Prepare the 'metadata' data frame ... OK >> Make the TranscriptDb object ... OK >> Warning messages: >> 1: In .normargSplicings(splicings, unique_tx_ids) : >> no CDS information for this TranscriptDb object >> 2: In .normargChrominfo(chrominfo, transcripts$tx_chrom, >> splicings$exon_chrom) : >> chromosome lengths and circularity flags are not available for this >> TranscriptDb object >> >> >>> txdb >>> >> TranscriptDb object: >> | Db type: TranscriptDb >> | Data source: BioMart >> | BioMart database: plant_mart_7 >> | BioMart database version: ENSEMBL PLANT 7 (EBI UK) >> | BioMart dataset: alyrata_eg_gene >> | BioMart dataset description: Arabidopsis lyrata genes (Araly1) >> | BioMart dataset version: Araly1 >> | Full dataset: yes >> | transcript_nrow: 32667 >> | exon_nrow: 174271 >> | cds_nrow: 0 >> | Db created by: GenomicFeatures package from Bioconductor >> | Creation time: 2010-12-11 17:43:13 -0800 (Sat, 11 Dec 2010) >> | GenomicFeatures version at creation time: 1.2.3 >> | RSQLite version at creation time: 0.9-4 >> | DBSCHEMAVERSION: 1.0 >> >> Just a reminder though that if you decide to use this then it's >> *crucial* that you align your RNA-seq data against the reference >> genome that corresponds to those annotations (I'm not sure which >> one it is, you'll need to investigate). >> >> Cheers, >> H. >> >> >>> Thanks, >>> Song Li >>> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages at fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> > > >