Question: Blast in metagenomics: should I download all NR database for this purpose?
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gravatar for fhsantanna
2.5 years ago by
fhsantanna440
Brazil
fhsantanna440 wrote:

Very basic question. I want to do a taxonomic analysis of an Iontorrent metagenomics data using MEGAN. I know that firstly I must blast the reads to a database (usually NR database from Genbank). I presume that this procedure should be done locally in order to process faster the data. So, I need to download all the NR database from Genbank. Is it correct?

blast metagenomics local • 1.5k views
ADD COMMENTlink written 2.5 years ago by fhsantanna440

You can do nt or nr. Take a look at the MEGAN manual before you do blast. You would want to use standard text or XML format output for blast.

ADD REPLYlink written 2.5 years ago by genomax64k

OK. But it should be local, right? Blasting directly to the server is not appropriate, isn't it?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by fhsantanna440
1

If you don't have a lot of reads you can go with the server.

ADD REPLYlink written 2.5 years ago by Picasa390

What is a lot of reads? I have 500k reads.

ADD REPLYlink written 2.5 years ago by fhsantanna440
1

NCBI server won't accept 500K reads in one go. If you are able, do the search locally. That way you will have control over it.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax64k
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