[BioC] Question about TranscriptDb and makeTranscriptDb method

[Song Li]

Hi Hervé ,

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
>



-- 
Postdoctoral Associate
Institute for Genome Sciences and Policy
Duke University