Hi Jen, I figured out a way to import bed file into DB. Please look at the table below.
*Sample Rows * binchromchromStartchromEndnamescorestrand585NC_00352166647191RL101000+ 585NC_00352172027900RL111000+ 585NC_00352179399021RL121000+ 585NC_0035219123 10124RL131000+ 585NC_003521912310124RL131000+ 585NC_0035211025610432UL21000+ 585NC_0035211050411097UL41000+ 585NC_0035211146911924UL51000+ 585NC_003521 1213012981UL61000+ 585NC_0035211305213693UL71000+ 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]> 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]>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
