Download Brachypodium Distachyon Genome

Question

[Sara]

Hi

I want to download the complete version of Brachypodium distachyon genome. How I can do that?

Thanks

Answer 1

[2184687-1231-83-]

wget ftp://ftp.ensemblgenomes.org/pub/plants/current/fasta/brachypodium_distachyon/dna/Brachypodium_distachyon.Brachy1.0.dna.toplevel.fa.gz

[Sara]

Hi Avilella, Thanks for your help. I am very new in the filed perhaps my question is stupid! I mapped the sequence against this genome but i dont have genomic coordination information of sequence. I have just scalfold name. how can i know if the read seq are mapped in intron or in exon?

another question: in the link you send to me, there are zip file also for each chromosome , what is the difefrences between toplevel and others? thanks

Answer 2

[Neilfws]

1. Search Google for "Brachypodium distachyon genome"
2. Select a suitable resource (or perhaps an alternative)
3. Find downloads link
4. Download appropriate files

[Michael]

That would work if the complete genome existed, but I think that genome is not finished yet, there is only the 8x assembly, that's maybe not a complete genome in the sense of the question.

[Neilfws]

Then maybe the answer is "you can't" :-) But the principle is the same.

[Michael]

But you are right, the page you found is the first hit from google. I don't really understand how somebody would miss to do exactly what you did first.

Answer 3

[Lyco]

A second possibitlity would be to read the paper on Brachypodium genome sequencing, published in Nature. Down at the bottom of the paper, the authors say that the whole genome sequence has been deposited in DDBJ/EMBL/GenBank, and they provide an accession number (ADDN01000000) which you can use for retrieval at one of those databases.

[Neilfws]

To be precise, they say "the whole-genome shotgun sequence"; that is, the scaffolds not the closed, finished genome.