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 >> >> >> >> >> >> >> >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
