Question: How to query the taxa IDs/GIs of a kraken database
0
gravatar for d.hand
12 months ago by
d.hand0
d.hand0 wrote:

I built a database from refSEQ in December, but my hits are missing a obvious genome.

Is there any easy way to extract a list of GIs used in the construction of a database or is this logged somewhere? Is there anyway to find out what subset of refseq kraken has built from?

sequencing • 379 views
ADD COMMENTlink written 12 months ago by d.hand0
1
gravatar for Sej Modha
12 months ago by
Sej Modha4.0k
Glasgow, UK
Sej Modha4.0k wrote:

seqid2taxid.map file in the Kraken DB directory contains the seqID and the taxonomy ID as two columns. If a database was built from scratch then the fasta files should be available in the library/added/*.fna in the Kraken DB folder.

ADD COMMENTlink modified 12 months ago • written 12 months ago by Sej Modha4.0k

What version of kraken are your using? I cannot find this fille, I'm using the standard build database which produces these fills:

database.kdb database.idx taxonomy/nodes.dmp taxonomy/names.dmp:

ADD REPLYlink modified 12 months ago • written 12 months ago by d.hand0
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