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ohlab / GRiD

Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).
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generating custum databases for grid multiplex mode #2

Closed till-bornemann closed 5 years ago

till-bornemann commented 5 years ago

Hi, I would like to use the 'grid multiplex' mode with custom genome databases instead of extending on the ones you supply. Can you use the update_database command to also generate new databases instead of extending on existing ones? When I tried using a database generated like this, I mostly get GRiD values between 1.00-1.10 not at all similar to iRep values. In single mode on the other hand, the GRid values make sense.

Any help is appreciated, Best regards Till

aemiol commented 5 years ago

Hi Till, Yes, it is perfectly Ok to use the 'update_database' to create your custom database. In that case, disregard any error warnings you may get. The first column in the generated 'database_misc.txt' will list the genomes in the new database