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