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]> 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]>> 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>". >> >> >> 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]>>> 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]>>>> 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]>>> >> >> 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]>>> 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]>>> >> >> [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
