Hi Diya, In the sample rows you provided, the value in your tenth column (blockCount) for all your sample rows is 1, indicating that each item only has one block. Additionally, the thickStart=chromStart and thickEnd=chromEnd for each item, which is why each of the items is displayed as "thick" from end to end.
Items with multiple blocks will have the a number greater than 1 for blockCount (the 10th column), a comma separated list of block sizes in the 11th column (blockSizes) and a comma separated list of the block start positions in the 12th column (blockStarts). Please see the following link for more details about the BED format and a sample of BED data with multiple blocks: http://genome.ucsc.edu/FAQ/FAQformat.html#format1.7 Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 10/12/11 1:24 PM, Dedeepya Vaka wrote: > Hi, > > > > Here I attached a figure from a paper who used UCSC genome browser viewer to > visualize their results. We want to reproduce our data in a similar fashion. > But I am not sure what they used a input to get the coverage information > > > > Thanks, > > > > Diya > > > > From: Dedeepya Vaka [mailto:[email protected]] > Sent: Wednesday, October 12, 2011 9:56 AM > To: '[email protected]' > Subject: BED detail format > > > > Hello UCSC, > > > > I am trying to upload a bed file with 12 columns. However I am not able to > see the block counts. When I view it in the browser I see no difference > between the 6 column and 12 column format. > > > > Here I am pasting the sample 12 column bed format. > > > > chrY 59031406 59031428 HWUSI-EAS000_29:1:107:13171:8952#0 > 25 + 59031406 59031428 255,0,0 1 22 0 > > chrY 59031877 59031894 HWUSI-EAS000_29:1:118:17184:2540#0 > 25 - 59031877 59031894 255,0,0 1 17 0 > > chrY 59032463 59032487 HWUSI-EAS000_29:1:102:8204:2058#0 > 25 - 59032463 59032487 255,0,0 1 24 0 > > chrY 59032532 59032553 HWUSI-EAS000_29:1:49:14535:7055#0 > 25 + 59032532 59032553 255,0,0 1 21 0 > > > > Your help is greatly appreciated. > > > > Thanks, > > > > Diya > > > > Data Analyst > > Cancer Biology Program > Sweet-Cordero Lab, Stanford University > http://sweetcorderolab.stanford.edu/ > > ph: 650.725.4802 > > > > > > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
