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Arabidopsis thaliana whole genome

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 :)

rna-seq alignment genome
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updated by GenoMax GenoMax • written by sangram_keshari sangram_keshari

1 answer

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

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written by GenoMax GenoMax

I guess Ensemble data also treated as standard??

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written by sangram_keshari sangram_keshari

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.

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written by GenoMax GenoMax

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