Genome Clade errors

[Lachlan Musicman]

After perusing the genomeClade table in the DB, I inserted the values of the genomes I was adding in the format:

D. repleta

D. hydei

D. birchii

But when I search the genomes, I get the error:

Warning/Error(s):

• Warning: central database genomeClade doesn't contain genome "Drosophila hydei"

Where is that error coming from? Or rather, why is it searching for the full name? What should I be changing to the full name to make this work?

cheers

L.

------
let's build quiet armies friends, let's march on their glass towers...let's build fallen cathedrals and make impractical plans

- GYBE

[Matthew Speir]

Hi Lachlan,

Thank you for your question about the error you're seeing with the genomeClade table in hgcentral. The Genome Browser code expects the same name for a particular assembly is used across a few different tables. For example, the name used in the "genome" column of the table dbDb should be the same as the one used in the "genome" column of the table genomeClade. If you used "Drosophila hydei" in dbDb.genome, then genomeClade.genome should also be "Drosophila hydei", not "D. hydei".

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

--

[Lachlan Musicman]

Thankyou - perfect!

------
let's build quiet armies friends, let's march on their glass towers...let's build fallen cathedrals and make impractical plans

- GYBE

[Lachlan Musicman]

Out of interest, which value does the hg.conf defaultGenome represent?

ie, should I have:

defaultGenome=Drosophila birchii

or
defaultGenome=D. birchii

cheers

L.

------
let's build quiet armies friends, let's march on their glass towers...let's build fallen cathedrals and make impractical plans

- GYBE

[Lachlan Musicman]

Ignore this, I read the docs :)

------
let's build quiet armies friends, let's march on their glass towers...let's build fallen cathedrals and make impractical plans

- GYBE