Question: Arabidopsis Araport11 genome annotation file
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gravatar for harrypotterandsbt
16 months ago by
harrypotterandsbt70 wrote:

Have anyone use Araport11 genome annotation file to replace TAIR10 genome annotation file?Because Araport11's GTF was released on 2016 ,which is newer than TAIR's GTF. And Araport11 also provide gene name,like "gene-id:AT1G01060; gene name"LHY" " I want to ask whether Araport11 is better for use as genome annotation file?

rna-seq genome • 682 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by harrypotterandsbt70

Thank you! Lieven.sterck.You answers really helps!

ADD REPLYlink written 16 months ago by harrypotterandsbt70
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Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

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ADD REPLYlink written 16 months ago by WouterDeCoster43k

Thank you for suggestion! I have accpted the helpful answer. Sorry,I'm new here and I will remeber your suggestion!

ADD REPLYlink written 16 months ago by harrypotterandsbt70
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gravatar for lieven.sterck
16 months ago by
lieven.sterck7.8k
VIB, Ghent, Belgium
lieven.sterck7.8k wrote:

that would be up to you to decide. The annotation provide by Araport11 is indeed newer than Tair10. They should be nonetheless interchangeable, however general rule is to use the one from which you also use the genomic sequence (though the genome for TAIR10 and Araport11 should be the same).

If Araport 11 suits your needs better then you can safely go for that one.

ADD COMMENTlink written 16 months ago by lieven.sterck7.8k
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