Hello Minou, The coordinate numbering is continuous across gaps, the locations of which are specified in the gap track as outlined by my colleague.
Best regards, Pauline Fujita, UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 09/21/11 07:58, Minou Bina wrote: > > Hi Greg > > I am just concerned about the numbering of nucleotides in regions that > include gaps > > My output consists of nucleotide position and then a motif > > 50 CGCG > 12000 CG > > etc > > > Minou Bina > > > > ----- Original Message ----- > From: "Greg Roe" <g...@soe.ucsc.edu> > To: "Minou Bina" <b...@purdue.edu> > Cc: genome@soe.ucsc.edu > Sent: Tuesday, September 20, 2011 7:35:06 PM > Subject: Re: [Genome] bed files for entire chromosomes > > Hi Minou, > > > Whole chromosome coordinates: for example, a 100 base long chromosome (e.g. > chr1:1-100) would be written like this in bed format: chr1 0 100 > > > The Gap table indicates gaps at teleomeres and centromeres. Examples: > chr1 0 10 10-base_telomere > chr1 399 500 100-base_centromere > chr1 89 100 10-base_telomere > > If you do not want your annotations to be in gaps, you can intersect your > annotations with the gap table using the table browser to see if they do have > annotations in the gaps: > > Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables > > - upload your bed (bigBed) file as a custom track and select it in the table > browser. > - click the intersect button and select: > group: mapping and seq. tracks > track: gap > - and submit > - choose and output format and submit > > > > Please let us know if you have any additional questions: genome@soe.ucsc.edu > > - > Greg Roe > UCSC Genome Bioinformatics Group > > > On 9/19/11 8:22 AM, Minou Bina wrote: > > Dear Katrina > > > Thank you for the info. > > Not clear how nucleotide numbering is handled for gaps and chromosome ends > when one uses the entire chromosomes to create bed files. > > How could one check for quality control? > > Minou Bina > > > > ----- Original Message ----- > From: "Katrina Learned" <katr...@soe.ucsc.edu> To: "Minou Bina" > <b...@purdue.edu> Cc: genome@soe.ucsc.edu Sent: Friday, September 16, 2011 > 7:11:18 PM > Subject: Re: [Genome] bed files for entire chromosomes > > Hi Minou, > > Here is some information about creating bed files: > http://genome.ucsc.edu/FAQ/FAQformat.html#format1 You might consider > converting your bed files to our bigBed format using the program bedToBigBed > . The main advantage of the bigBed files is that only the portions of the > files needed to display a particular region are transferred to UCSC, so for > large data sets bigBed is considerably faster than regular bed files. The > bigBed file remains on your web accessible server (http, https, or ftp), not > on the UCSC server. > > I am not sure if this is what you were asking, but to specify a block to > cover the entire chromosome, you would set your chromStart to 0 and your > chromEnd to the length of the chromosome. To find out the length of each > chromosome, from the gateway page ( http://genome.ucsc.edu/cgi-bin/hgGateway > ), use the drop-down menus to select your assembly of interest, and under the > drop-downs, in the light blue bar that states, " About the <assembly > information> (sequences)", click on the 'sequences' link. For example, the > hg19 sequences link would take you here: > http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&chromInfoPage= I hope this > information is helpful. Please contact the mail list ( genome@soe.ucsc.edu ) > again if you have any further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > On 9/16/11 12:58 PM, Minou Bina wrote: > > Hi > > We are planning to analyze entire human chromosomes and create .bed files for > display on the human genome browser. > > It is clear how we should specify the block position for an entire chromosome > and how we should do the numbering. > > Minou Bina > Purdue University > _______________________________________________ > Genome maillist - Genome@soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - Genome@soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - Genome@soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - Genome@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
