doc: organism search database naming

[alpapan]

The correct way to implement both blat and blast is to ensure that the 'search database' for the organism is: a) full path to the 2bit file b) blast databases are suffixed on the 2bit file

e.g. this

naturalis_ragout2_final.2bit
naturalis_ragout2_final.2bit.nhd
naturalis_ragout2_final.2bit.nhi
naturalis_ragout2_final.2bit.nhr
naturalis_ragout2_final.2bit.nin
naturalis_ragout2_final.2bit.nog
naturalis_ragout2_final.2bit.nsd
naturalis_ragout2_final.2bit.nsi
naturalis_ragout2_final.2bit.nsq

to create them, do this:

faToTwoBit fasta fasta.2bit
makeblastdb -dbtype nucl -in fasta -out fasta.2bit

any other way and either blat or blast will (silently) fail

[nathandunn]

Alexie,

I’m only doing this automatically via docker. Where you creating a suggestions for doc?

If you want to add this bit to the doc, you can just edit directly to create a PR here: https://github.com/GMOD/Apollo/blob/develop/docs/Configure.md#search-tools https://github.com/GMOD/Apollo/blob/develop/docs/Configure.md#search-tools

And I can merge it into the doc. I think this is good clarification, though.

Nathan

On Dec 20, 2020, at 11:36 PM, Alexie Papanicolaou [email protected] wrote:

The correct way to implement both blat and blast is to ensure that the 'search database' for the organism is: a) full path to the 2bit file b) blast databases are suffixed on the 2bit file

e.g. this

naturalis_ragout2_final.2bit naturalis_ragout2_final.2bit.nhd naturalis_ragout2_final.2bit.nhi naturalis_ragout2_final.2bit.nhr naturalis_ragout2_final.2bit.nin naturalis_ragout2_final.2bit.nog naturalis_ragout2_final.2bit.nsd naturalis_ragout2_final.2bit.nsi naturalis_ragout2_final.2bit.nsq to create them, do this:

faToTwoBit fasta fasta.2bit makeblastdb -dbtype nucl -in fasta -out fasta.2bit any other way and either blat or blast will (silently) fail

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