Hello Tiandao,
This is the correct setup for these two tables. Another key table is
dbDb (see step #11):
http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database
If you are still having problems after following the instructions, then
it is hard to know the exact cause. Duplicating what you did before for
other successfully loaded assemblies is recommended.
Regards,
Jen
UCSC Genome Browser Support
On 7/17/10 11:45 AM, Tiandao Li wrote:
> 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]
> <mailto:[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]
> <mailto:[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]>
> <mailto:[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]>>
> <mailto:[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]>>
> <mailto:[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]>>>
> <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,
>
> 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>
> <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]>>>>
> <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:
>
> 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]>>>>>
> <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] <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]>>>>>
> <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]
> <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]>>>>>
> <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]
> <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]>>>>>
> <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] <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]>>>>>
> <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]
> <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
>
>
>
>
>
>
>
>
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
