Thanks Hiram,
This seems to work but what are the tables in the proteinsX db, I
haven't been able to find any info on what each table holds.
Thank you
Jay
On Apr 1, 2010, at 1:11 PM, Hiram Clawson wrote:
> For a quick work-around since this isn't a genome that actually needs this
> particular database, try simply creating an empty database:
>
> $ hgsql -e "create database proteins040315;" mysql
>
> If that doesn't work, download the actual protein databases, from, for
> example:
> ftp://hgdownload.cse.ucsc.edu/mysql/proteins040315/
> or text dumps:
> ftp://hgdownload.cse.ucsc.edu/goldenPath/proteinDB/proteins040315/database/
> or rsync
> rsync -avz --progress rsync://hgdownload.cse.ucsc.edu/mysql/proteins/040315/
> or
> sync -avz --progress
> rsync://hgdownload.cse.ucsc.edu/goldenPath/proteinDB/proteins040315/database/
>
> It may need the other protein databases too.
>
> --Hiram
>
> Jaysheel Bhavsar wrote:
>> Hi Hiram,
>> I am not sure if that is what need to be done hear, I am not yet
>> familiar with the browsers working. When it get to the "base" level of the
>> view, and click on a region of the bed file that I uploaded, I get the
>> following error message
>> Couldn't connect to database proteins040315 on xxxx.edu as yyyy. Unknown
>> database 'proteins040315'
>> (xxxx= host name, and yyyy=usename for mysql)
>> how are the proteinsX tables create? I understand that system is looking
>> for proteins040315 database because that is what 'default' points to in
>> gdbPdb table.
>> Does this help?
>> Thank you
>> Jay
>> On Apr 1, 2010, at 11:57 AM, Hiram Clawson wrote:
>>> Good Morning Jay:
>>>
>>> It isn't clear what you are referring to here.
>>>
>>> Do you say you have protein sequences that you want to load into the genome
>>> browser ?
>>>
>>> To do that, you need to align the proteins to the genome with an aligner,
>>> for example blat. Once you have those positions as psl files, you can load
>>> the psl file as a track in the genome browser.
>>>
>>> --Hiram
>>>
>>> Jaysheel Bhavsar wrote:
>>>> Hi guys,
>>>> I am very new at this genome viewer business, so please bare with me if
>>>> I don't have the terminology or understanding of the inner workings. I
>>>> need to get genome browser up and running for genome that we have in the
>>>> lab. I have been able to get a local copy of genome browser up and
>>>> running, and have been able to add a custom track, along with gc5Base, and
>>>> wiggle info as described here
>>>> (http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database).
>>>> Everything seem to work as expected (I haven't played around with all the
>>>> options in trackDb.ra, but that will come later).
>>>> Issue 1:
>>>> Now the issue is that I am not able to get to the actually proteins/seq
>>>> for the tracks loaded. From what I understand I can create an entry in
>>>> gdbPdb, which seems straight forward (insert statement with org db name
>>>> like hg18 and proteinsX name). But I can't see find information as to
>>>> what needs to be in proteinesX database. I wasn't able find a utility or
>>>> hgX loader script either (unless I missed it). Could someone please point
>>>> me in the right direction, as to how to upload my protein/seq data.
>>>> Issue 2:
>>>> I have some metadata associated with each chromosome that I loaded into
>>>> db, is there a way to show that info on the browser? I have a tab
>>>> delimited file of protein id, gotermId and go annotations.
>>>> Thank you Jay
>
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