Question: how to determine Genome and Gene ID in goseq for wheat
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gravatar for muhammadaqeel24
3 months ago by
muhammadaqeel240 wrote:

Hi, I am working on wheat RNA seq data.I have found differential expressed genes in wheat. Now I want to do gene ontology by using GOseq R package. This package take the genome ids as given in manual

pwf=nullp(genes,"hg19","ensGene")

hg19 is for human. but I could not found this type of genome id for Wheat. Can anyone tell me which one is used for wheat?

ADD COMMENTlink modified 3 months ago by i.sudbery5.3k • written 3 months ago by muhammadaqeel240
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gravatar for i.sudbery
3 months ago by
i.sudbery5.3k
Sheffield, UK
i.sudbery5.3k wrote:

You can use supportedOrganisms() to get a list of genomes that are supported and their IDs. However, I would be surprised if goseq had this available for wheat, in which case you'll have to supply the bias.data and the category mappings yourself. See section 5 of the GOSeq manual. In this case you'd supply the bias.data to nullp directly, rather than via genome and gene id type:

pwf <- nullp(genes, bais.data = my_length_vector)
ADD COMMENTlink written 3 months ago by i.sudbery5.3k

Where we can get category mappings as these are not available

ADD REPLYlink written 3 months ago by muhammadaqeel240

You can use bioMart. Go to plants.ensembl.org and select bioMart, Wheat as the the genome, and then under features/external you can select GO accession.

ADD REPLYlink written 3 months ago by i.sudbery5.3k
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