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
