Question: Arabidopsis Araport11 genome annotation file
0
gravatar for harrypotterandsbt
3 months ago by
harrypotterandsbt10 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 • 276 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by harrypotterandsbt10

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

ADD REPLYlink written 3 months ago by harrypotterandsbt10
1

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.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 3 months ago by WouterDeCoster39k

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

ADD REPLYlink written 3 months ago by harrypotterandsbt10
3
gravatar for lieven.sterck
3 months ago by
lieven.sterck4.8k
VIB, Ghent, Belgium
lieven.sterck4.8k 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 3 months ago by lieven.sterck4.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 798 users visited in the last hour