Hello, One of our engineers provided an alternate solution:
Instead of naming your defined regions, you could use the tools at Galaxy, http://main.g2.bx.psu.edu/, which works in conjunction with the Table Browser, to join your regions with the Txn Factor ChIP data. See the "Join the intervals of two datasets side-by-side" tool in the "Operate on Genomic Intervals" section. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 10/3/11 3:13 PM, Katrina Learned wrote: > Hello, > > Unfortunately, the 'name' field will not show up in your results. Here > is an excerpt from the page on which defined regions are entered: > > "The fourth field, name, is optional and for notation purposes only, it > is not used in the table browser." > > Please contact the mail list ([email protected]) again if you have any > further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > > > On 10/3/11 3:32 AM, 郭志云 wrote: >> hello UCSC, >> Thank you very much! But according to the method which you provide I still >> did not solve my problem. >> For a query search example: >> >> clade:Mammal >> genome:Human >> assembly:hg19 >> group:Regulation >> track:Txn Factor ChIP >> table:wgEncodeRegTfbsClustered >> define regions: >> chrX 151073054 151077000 name1 >> chrX 151183000 151200000 name2 >> output format:all fields from selected table >> >> but I can not find the "name1" and "name2" in the result. How can I get >> the result including my defined name:"name1" and "name2"? Thank you! >> >> The result is below, also is available in the attached file: >> >> #bin chrom chromStart chromEnd name score strand >> thickStart thickEnd reserved blockCount blockSizes >> chromStarts expCount expIds expScores >> 1737 chrX 151073520 151073824 NF-YA 111 . >> 151073520 151073824 0 1 304 0 95 >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94, >> >> 0,0,0,0,0,0,0,0,111,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, >> 1737 chrX 151073550 151073743 NF-YB 159 . >> 151073550 151073743 0 1 193 0 95 >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94, >> >> 0,0,0,0,0,0,0,0,159,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, >> 1738 chrX 151194601 151194845 CEBPB 91 . >> 151194601 151194845 0 1 244 0 95 >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94, >> >> 0,0,91,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, >> 1738 chrX 151194976 151195216 MafK_(ab50322) 115 >> . 151194976 151195216 0 1 240 0 95 >> >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94, >> >> 0,0,0,115,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, >> 1738 chrX 151195921 151196121 E2F6_(H-50) 140 >> . 151195921 151196121 0 1 200 0 95 >> >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94, >> >> 0,0,0,0,0,0,0,0,140,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, >> 1738 chrX 151197024 151197314 STAT3 239 . >> 151197024 151197314 0 1 290 0 95 >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94, >> >> 0,0,239,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, >> 1738 chrX 151197044 151197350 CEBPB 1000 . >> 151197044 151197350 0 1 306 0 95 >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94, >> >> 0,0,1000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, >> 1738 chrX 151197044 151197328 p300_(N-15) 409 >> . 151197044 151197328 0 1 284 0 95 >> >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94, >> >> 0,0,409,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, >> 1738 chrX 151199900 151200150 TAL1_(SC-12984) 105 >> . 151199900 151200150 0 1 250 0 95 >> >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94, >> >> 0,0,0,0,0,0,0,0,105,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, >>> >>> >>> >>> >>> >>>> -----原始邮件----- >>>> 发件人: "Pauline Fujita"<[email protected]> >>>> 发送时间: 2011年10月1日 星期六 >>>> 收件人: "郭志云"<[email protected]> >>>> 抄送: genome<[email protected]> >>>> 主题: Re: [Genome] about defined regions of Table Browser >>>> >>>> Hello, >>>> >>>> In order for your file to be recognized as a BED4 file (and thereby >>>> include the 4th column in your output) all lines must include something >>>> in the 4th column. You will need to put something even in the rows that >>>> you don't want to name (i.e. a period or the empty string could be used >>>> there -- so there will be a tab character after the end coordinate, and >>>> then a newline.) For example: >>>> >>>> chrX 151073054 151173000 . >>>> chrX 151183000 151190000 optionalRegionName >>>> chrX 151283000 151290000 . >>>> chrX 151383000 151390000 . >>>> >>>> >>>> Hopefully this information was helpful and answers your question. If you >>>> have further questions or require clarification feel free to contact the >>>> mailing list [email protected]. >>>> >>>> Best regards, >>>> >>>> Pauline Fujita >>>> >>>> UCSC Genome Bioinformatics Group >>>> http://genome.ucsc.edu >>>> >>>> On 9/27/11 9:59 PM, 郭志云 wrote: >>>>> Region definitions are ordinary 3- or 4-field bed file format. For >>>>> example: >>>>> >>>>> # comment lines can be included starting with the # symbol >>>>> chrX 151073054 151173000 >>>>> chrX 151183000 151190000 optionalRegionName >>>>> chrX 151283000 151290000 >>>>> chrX 151383000 151390000 >>>>> >>>>> There is a limit of 1,000 defined regions. Using the upload file function >>>>> will replace any existing regions. The fourth field, name, is optional >>>>> and for notation purposes only, it is not used in the table browser. >>>>> >>>>> Question: If I want to display the RegionName in the result of table >>>>> browser, how should I do? Because if I have too many defined region, I >>>>> hardly find the results of the corresponding defined region. How can I >>>>> distinguish the results of each defined region. >>>>> _______________________________________________ >>>>> Genome maillist [email protected] >>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> _______________________________________________ >> Genome maillist [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
