Here is the sample of defaultDb and genomeClade input.
INSERT INTO defaultDb (genome, name) VALUES ("CCMV_NC_003521",
"CCMV_NC_003521");
INSERT INTO genomeClade (genome, clade, priority) VALUES ("CCMV_NC_003521",
"other", 7);
On Fri, Jul 16, 2010 at 3:07 PM, Tiandao Li <[email protected]> wrote:
> Yes. And so if I select Mammal again, it won't bring up Human. This is a
> human hg18 only genome browser. I checked dbDb, defaultDb, and genomeClade,
> no problem there for me. And I use the "add custom tracks" button, and
> direct me to another upload track page, I used clade there to select
> different genomes, no problem there.
>
>
> On Fri, Jul 16, 2010 at 2:53 PM, Jennifer Jackson <[email protected]>wrote:
>
>> Hi Tiandao,
>>
>> This could be a set-up problem in hgcentral if you assigned one of your
>> loaded databases to the clade "Other". Were the defaultDb and genomeClade
>> tables modified as in step #12 of this help wiki?
>>
>>
>> http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database
>>
>> Thank you,
>>
>>
>> Jen
>> UCSC Genome Browser Support
>>
>> On 7/16/10 10:24 AM, Tiandao Li wrote:
>>
>>> Hi Jen,
>>>
>>> Finally I imported all genomes and annotation files into local genome
>>> browser. However, when select Other (clade), the page always show the
>>> error mesg. Would you please what caused this error, and how to fix it?
>>> Thanks!
>>>
>>>
>>> *Error(s):*
>>>
>>> * Error reading 5 bytes: Operation not permitted
>>>
>>>
>>> On Thu, Jul 15, 2010 at 12:04 AM, Jennifer Jackson <[email protected]
>>> <mailto:[email protected]>> wrote:
>>>
>>> Hello Tiandao,
>>>
>>> Are you still having trouble with your mirror? I am not sure which
>>> problems were sorted out already and which you would still like help
>>> with.
>>>
>>> For your track below, have you tried setting the display to "pack"
>>> or "full" in the assembly browser display? To do this, use the pull
>>> down menu under the track name.
>>>
>>> More display help:
>>>
>>> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning
>>>
>>> File format help (including .wig):
>>> http://genome.ucsc.edu/FAQ/FAQformat.html
>>>
>>> Regarding the trackDb table - this is required. Lines in the table
>>> correspond to tracks in the assembly.
>>>
>>>
>>> Hopefully this helps,
>>>
>>> Jen
>>> UCSC Genome Browser Support
>>>
>>> On 7/14/10 9:29 AM, Tiandao Li wrote:
>>>
>>> Hi Jen,
>>>
>>> I figured out a way to import bed file into DB. Please look at
>>> the table
>>> below.
>>>
>>> *Sample Rows *
>>>
>>>
>>>
>>> bin chrom chromStart chromEnd name score
>>> strand
>>> 585 NC_003521 6664 7191 RL10 1000 +
>>> 585 NC_003521 7202 7900 RL11 1000 +
>>> 585 NC_003521 7939 9021 RL12 1000 +
>>> 585 NC_003521 9123 10124 RL13 1000 +
>>> 585 NC_003521 9123 10124 RL13 1000 +
>>> 585 NC_003521 10256 10432 UL2 1000 +
>>> 585 NC_003521 10504 11097 UL4 1000 +
>>> 585 NC_003521 11469 11924 UL5 1000 +
>>> 585 NC_003521 12130 12981 UL6 1000 +
>>> 585 NC_003521 13052 13693 UL7 1000 +
>>>
>>>
>>> The problem is I can't show the name next to the bar. Please help!
>>>
>>> On Wed, Jul 14, 2010 at 10:32 AM, Tiandao Li <[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>> wrote:
>>>
>>> Hi Jen,
>>>
>>> I followed your advice, however, the converted wig file
>>> contains no
>>> annotated info, such as RL10 in the last column.
>>>
>>> Regarding gc5Base generation in building new genome, from
>>> the help
>>> manual, looks like it needs at least one trackDb to show the
>>> genome.
>>> Is there a way to check on the genome on browser without any
>>> trackDb, anyway, there are 3 default trackDbs there, Base
>>> Position,
>>> Short Match, and Restr Enzymes.
>>>
>>> Thanks,
>>>
>>> Tiandao
>>>
>>>
>>> On Tue, Jul 13, 2010 at 4:48 PM, Jennifer Jackson
>>> <[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>> wrote:
>>>
>>> Hello Tiandao,
>>>
>>> Try these two modifications:
>>> 1) remove the track line from the file
>>> 2) leave off all arguments to the sort command (the
>>> numerical
>>> sort is not wanted)
>>>
>>> sort bedFile.bed | bedItemOverlapCount [options]
>>> <database> stdin
>>>
>>> A new assembly requires the six files listed in this
>>> help document:
>>> http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation
>>>
>>> It would be OK to skip step #10 in this help document:
>>>
>>> http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database
>>>
>>> Thanks,
>>>
>>>
>>> Jen
>>> UCSC Genome Browser Support
>>>
>>> On 7/13/10 12:19 PM, Tiandao Li wrote:
>>>
>>> Hi Jen,
>>>
>>> However, it still showed the wrong mesg. The file is
>>> tab
>>> separated.
>>>
>>> $ more ccmv.bed
>>> track color=125,0,0
>>> NC_003521 6664 7191 RL10
>>> NC_003521 7202 7900 RL11
>>> NC_003521 7939 9021 RL12
>>> NC_003521 9123 10124 RL13
>>> NC_003521 9123 10124 RL13
>>> NC_003521 10256 10432 UL2
>>> NC_003521 10504 11097 UL4
>>> NC_003521 11469 11924 UL5
>>> NC_003521 12130 12981 UL6
>>> NC_003521 13052 13693 UL7
>>> NC_003521 13799 14305 UL8
>>>
>>> $ sort -k1,1 -k2,2n ccmv.bed |
>>> /opt/kent/bedItemOverlapCount
>>> ccmv stdin
>>> Expecting 3 words line 12 of stdin got 2
>>>
>>> And would you explain why need to generate gc5Base
>>> data and
>>> load table
>>> during building custom geome db?
>>>
>>> Thanks,
>>>
>>> Tiandao
>>>
>>> On Tue, Jul 13, 2010 at 1:55 PM, Jennifer Jackson
>>> <[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>> wrote:
>>>
>>> Hello Tiandao,
>>>
>>> Use the database name that you assigned to your
>>> reference genome
>>> when it was loaded. This is the same value as in
>>> "hgcentral.dbDb.name <http://hgcentral.dbDb.name>
>>> <http://hgcentral.dbDb.name>
>>> <http://hgcentral.dbDb.name>".
>>>
>>>
>>> Hopefully this helps,
>>>
>>>
>>> Jen
>>> UCSC Genome Browser Support
>>>
>>> On 7/13/10 8:33 AM, Tiandao Li wrote:
>>>
>>> Hi Jen,
>>>
>>> I have no problem to create and load
>>> trackDb. I want
>>> to use BED
>>> for our
>>> genome annotation. The following is my bed
>>> file.
>>>
>>> $ more ccmv.bed
>>> track name=CMV color=125,0,0
>>> NC_003521 6664 7191 RL10
>>> NC_003521 7202 7900 RL11
>>> NC_003521 7939 9021 RL12
>>> NC_003521 9123 10124 RL13
>>> NC_003521 9123 10124 RL13
>>> NC_003521 10256 10432 UL2
>>> NC_003521 10504 11097 UL4
>>> NC_003521 11469 11924 UL5
>>> NC_003521 12130 12981 UL6
>>> NC_003521 13052 13693 UL7
>>> NC_003521 13799 14305 UL8
>>> NC_003521 14327 14860 UL9
>>>
>>>
>>> sort -k1,1 -k2,2n bedFile.bed \
>>> | bedItemOverlapCount [options]
>>> <database> stdin \
>>> | wigEncode stdin data.wig data.wib
>>>
>>> However, I didn't know which database I
>>> should input for
>>> bedItemOverlapCount. Or any alternative method
>>> directly convert
>>> bed to
>>> wig, which I knew how to upload.
>>>
>>> Thanks,
>>>
>>> Tiandao
>>>
>>> On Mon, Jul 12, 2010 at 11:02 PM, Jennifer
>>> Jackson
>>> <[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>>> wrote:
>>>
>>> Hello Tiandao,
>>>
>>> The README file I pointed you to has the
>>> instructions for
>>> creating a
>>> track. Did you have a question about a
>>> particular step?
>>>
>>> Or maybe the problem is related to track
>>> type?
>>> The RefSeq Genes
>>> track type is "genePred". It might be
>>> good to
>>> examine the
>>> current
>>> hg19 trackDb.ra file in the kent source
>>> tree to
>>> see how
>>> RefSeq Genes
>>> is set up there.
>>>
>>> Or maybe the problem is understanding the
>>> viewing options? A
>>> PSL,
>>> BED, and genePred track type all look a
>>> bit
>>> similar in the
>>> browser
>>> display. Dense mode will put all data on
>>> the
>>> same line. Both
>>> pack
>>> and full will display one line per
>>> table/file
>>> (where one line
>>> usually represents the alignment of a
>>> entire
>>> sequence). To
>>> see this,
>>> open the RefSeq Gene track in the
>>> browser and
>>> switch between the
>>> different display modes using the
>>> pull-down menu
>>> under the
>>> track name.
>>>
>>> Some display help:
>>>
>>> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#FineTuning
>>>
>>> Hopefully this helps, but if not please
>>> let us know.
>>>
>>> Best regards,
>>>
>>> Jen
>>> UCSC Genome Browser Support
>>>
>>> On 7/12/10 8:40 AM, Tiandao Li wrote:
>>>
>>> Hi,
>>>
>>> I searched through genome and
>>> genome-mirror
>>> lists about
>>> how to add
>>> annotation info (such as CDS) to
>>> genome
>>> database on local
>>> mirror. Where
>>> can I find actual examples of
>>> trackDb.ra to load
>>> annotation info to
>>> local mirror?
>>>
>>> Thanks,
>>>
>>> Tiandao
>>>
>>> On Tue, Jul 6, 2010 at 4:38 PM,
>>> Jennifer Jackson
>>> <[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>>>> wrote:
>>>
>>> Hi Tiandao,
>>>
>>> For genomes with annotation, the
>>> path
>>> would be:
>>>
>>> 1) load the reference genome
>>> sequence as
>>> you have done
>>> previously
>>> 2) layer in annotation as tracks
>>> mapped
>>> to the
>>> genome in #1
>>>
>>> This README in the kent source
>>> tree has
>>> the details
>>> for #2
>>> kent/src/product/README.trackDb
>>>
>>> I hope this pointer is useful, but
>>> please let us
>>> know if you
>>> need
>>> more help.
>>>
>>> For next time, it would nice for
>>> us if
>>> you sent your
>>> question
>>> through one our mailing lists.
>>> This
>>> question would
>>> be a good
>>> fit for
>>> the [email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>>>>
>>>
>>> list. Doing this would help us
>>> to get
>>> you a speedy
>>> answer
>>> and also
>>> help other users that are
>>> reviewing the
>>> Q & A on the
>>> public
>>> posting.
>>> If you need private (not posted)
>>> communications, the
>>> list
>>> [email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]
>>> >>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]
>>> >>>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]
>>> >>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>>>> would be an
>>>
>>> alternative as it is internal to
>>> the
>>> UCSC Browser
>>> team only.
>>>
>>> Best regards,
>>> Jen
>>>
>>> UCSC Genome Browser Support
>>> http://genome.ucsc.edu/contacts.html
>>> [email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>
>>> <mailto:[email protected] <mailto:[email protected]>
>>> <mailto:[email protected] <mailto:[email protected]>>>>>
>>>
>>> [email protected] <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>
>>> <mailto:[email protected]
>>> <mailto:[email protected]>>>>>
>>>
>>>
>>>
>>> On 7/6/10 1:00 PM, Tiandao Li
>>> wrote:
>>>
>>> Hi Jen,
>>>
>>> We have several annotated
>>> genomes of
>>> viruses
>>> download
>>> from NCBI and
>>> other DB serves. Now I want to
>>> import them with
>>> annotation into our
>>> local genome browser. Would
>>> you
>>> please point me
>>> to the
>>> details
>>> of how to
>>> do it? I import some
>>> sequences without
>>> annotation to our
>>> browser
>>> before.
>>>
>>> Thanks,
>>>
>>> Tiandao
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>
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