Question: How to Extract Bacteria From Ncbi Nt.
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4.7 years ago

I want to extract bacteria from ncbi nt to make a bacteria subset nt database. And use bowtie2 mapping reads with this bacteria subset nt database.

I have find some information at "Vertebrate Subset Nr Database? Build My Own?". I just don't know what I can do now. Many information teach my to use formatdb or blastdbcmd. But it's no use know. NCBI has (or is about to) stopped supporting gi numbers.

Can you give me some information?

genome RNA-Seq rna-seq sequence • 1.6k views
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If you are only looking to identify bacteria then you could try the 16S bacterial blast database indexes that NCBI makes available.

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Thank, I will try it.

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I change 16S bacterial to fasta, and use it on bowtie2, but I got 0.07% overall alignment rate.

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