Question: How to Extract Bacteria From Ncbi Nt.

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8.3 years ago

felix.kuo.1211 ▴ 10

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 • 2.6k views

ADD COMMENT • link updated 7.7 years ago by Biostar 20 • written 8.3 years ago by felix.kuo.1211 ▴ 10

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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.

ADD REPLY • link 8.3 years ago by GenoMax 148k

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Thank, I will try it.

ADD REPLY • link 8.3 years ago by felix.kuo.1211 ▴ 10

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

ADD REPLY • link 8.3 years ago by felix.kuo.1211 ▴ 10

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