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?
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.