Re: [Genome] import annotated genome

[Jennifer Jackson]

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 <j...@soe.ucsc.edu
> <mailto:j...@soe.ucsc.edu>> 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 <lit...@gmail.com
>         <mailto:lit...@gmail.com>
>         <mailto:lit...@gmail.com <mailto:lit...@gmail.com>>> 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
>         <j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>> 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
>         <j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>>> 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
>         <j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>>>> 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
>         <j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>
>         <mailto:j...@soe.ucsc.edu <mailto:j...@soe.ucsc.edu>>>>>> 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 genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>>>>
>
>                                         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
>         genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>>>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>>>>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>>>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>>
>         <mailto:genome-...@soe.ucsc.edu <mailto:genome-...@soe.ucsc.edu>
>         <mailto:genome-...@soe.ucsc.edu
>         <mailto:genome-...@soe.ucsc.edu>>>>> 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
>         gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>>>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
>         <mailto:gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>>>>>
>
>         genome-mir...@soe.ucsc.edu <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>
>         <mailto:genome-mir...@soe.ucsc.edu
>         <mailto:genome-mir...@soe.ucsc.edu>>>>>
>
>
>
>                                         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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