Arabidopsis thaliana whole genome

Question

[sangram_keshari]

Please correct me if I am wrong.

I wan to align my set of RNA-seq reads into Arabidopsis thaliana genome. So where would I get the FASTA file of this?

I looked for the [Ensemble FTP][1] and downloaded the file - Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz

Is this the correct genome file to start the alignment or should I get it from somewhere else like TAIR. But in TAIR also its confusing which one to download.

Can anyone please help me with this. Thank You :)

Answer 1

[GenoMax]

Get the sequence/annotation/aligner index bundle from iGenomes site.

[sangram_keshari]

I guess Ensemble data also treated as standard??

[GenoMax]

Primary sequence data comes from the genome project. Ensembl may have additional annotation but otherwise everything should be the same.

You could also use Araport to get the sequence/annotations. You would need to build your own indexes.