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Question: GoSeq: use ENSEMBLTRANS as input
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gravatar for idomtamir
3.4 years ago by
idomtamir10
Austria
idomtamir10 wrote:

Hi,

I am thinking about switching from GoStats to GoSeq. Is there a built in possibility to use the ENSEMBL transcript annotation or can I only use ENSEMBL genes? Do I have to annotate myself the transcripts with the gene go category + length?

 

> subset(supportedGenomes(), species == "Human" & db == "hg19")
    db species      date                               name
2 hg19   Human Feb. 2009 Genome Reference Consortium GRCh37
                                                              AvailableGeneIDs

2 ccdsGene,ensGene,exoniphy,geneSymbol,knownGene,nscanGene,refGene,xenoRefGene

 

 

ADD COMMENTlink modified 3.4 years ago by Nadia Davidson270 • written 3.4 years ago by idomtamir10
2
gravatar for Nadia Davidson
3.4 years ago by
Australia
Nadia Davidson270 wrote:

Hi,

Only the gene level information is supported, so you would have to specify the go terms and lengths manually if you want to use transcripts instead. 

Cheers, 

Nadia.

 

 

ADD COMMENTlink written 3.4 years ago by Nadia Davidson270
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