nt database Blast

Question

[Giulia.cosenza]

Hi guys,

I want to use BLAST for my metagenome Taxonomy analysis and than MEGAN6.
Do I have to download the database I want (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) or is that a way to performe the classification on a server without downloading the huge amount of data? In the MEGAN6 slides I found within the tutorial documentation it seems like the program performs the classification on a server and just give me back the results, but looking at tutorials on the internet I only saw people downloading the db on their PC.

Thank you all.

[GenoMax]

Giulia.cosenza : Please follow up on your past questions. Up-voting answers/comments that help and accepting answers (green check mark) is the way to do this.

Answer 1

[lennykovac]

You have to got the database somewhere... Either local on your machine, where you downloaded it, or on a server where you have access to.

[Giulia.cosenza]

thank you! I have another question: I have a shot gun sequencing output in fastq format and I upload it on blastn but when I start the analysis I get an ERROR and no results, I immagine because the file is to big....so how can I classify the reads with blast?

[lennykovac]

As far as I know the default blastn does not support fastq files. If you would read the Docs:

The data may be either a list of database accession numbers, NCBI gi numbers, or sequences in FASTA format.

I can only emphasis that you read the documentation. You wont get very far in the future if you keep asking unnecessary questions, instead of reading the bare minimum of documentation.

[Giulia.cosenza]

I should probably have put the question in another way since of cource I know fastq is not supported (I converted it in fasta but get a error about the dimension of the file). By the way I'm sorry if my questions could have bothered someone, I obviously didn't mean to, I was just looking for some help since I still struggle with documentation in english. There are very few 'unecessary' or 'studpid' question when someone is just trying to learn something. I didn't force anyone to answer my questions, so if they seem like a waste of time just don't mind them, but there is absolutely no need to mortify others.

[GenoMax]

DIAMOND (or for that matter even BLAST+ with nr) requires significant memory and disk resources to run. If you don't have access to a server then this analysis may be difficult to do locally. I am not aware of a public DIAMOND server where you can upload your data but perhaps someone may know of one.