[BioC] Celegans.db_2.3.5: Wormbase version

[Zhu, Julie]

Hi Marc,

Thank you very much for the quick response and detailed explanation! We used
the package last year. The paper is almost ready to be submitted, so we will
most likely keep the annotation as it is.

According to http://hgdownload.cse.ucsc.edu/downloads.html#c_elegans, it was
updated to ce6 on May 2008.

Thanks again for your help!

Kind regards,

Julie



On 9/2/10 8:13 PM, "Marc Carlson" <mcarlson at fhcrc.org> wrote:

> Hi Julie,
> 
> Unfortunately, the 2.3.5 packages are old enough that we were not yet
> stamping that information into the manual pages.  I can tell you that it
> was built with what was the most recent version for celegans that UCSC
> had "at that time", and that the vintage means that this package was
> built around this time one year ago.  So if you really need to track it
> down, you might be able to get that information from UCSC.
> 
> But a better option is to use more current annotation packages.  If you
> are willing to upgrade to the latest version (released just last
> spring), then you will notice that the data about what build was used
> has been improved to be much more specific.:
> 
> So for 2.4.1, if you look at the manual page for a mapping that is
> impacted by UCSC data you will notice that it is much more specific
> now.  So:
> 
> ?celegansCHRLOC
> 
> will show that it was built with:
> 
> ftp://hgdownload.cse.ucsc.edu/goldenPath/ce6
> 
> 
> Hope this helps you,
> 
> 
>   Marc
> 
> 
> 
> On 09/02/2010 01:57 PM, Zhu, Julie wrote:
>> Hi,
>> 
>> I used celegans.db_2.3.5 to convert affy ID to WormBaseID. Could you please
>> let me know the version of wormbase (e.g. WS180, WS200, etc..) that was used
>> for celegans.db_2.3.5?
>> 
>> Thank you very much for your help!
>> 
>> Kind regards,
>> 
>> Julie
>> 
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