Retrieve Information From Ucsc Genome Browser ?

Question

[khikho]

For each chromosome of my sample I draw a cnv plot but I want to retrieve the CNV region (CNV value, type, starting and Ending point) which is in the UCSC genome browser for that chromosome and then add that region on my plot to test the system. Do you have any suggestion!?

Answer 1

[Pierre Lindenbaum]

AS far as I can see, this information is located in the gdv table at the ucsc:

~$ mysql  --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 \
      -e 'select * from dgv\G'

*************************** 1. row ***************************
       bin: 73
     chrom: chr1
chromStart: 10376
  chromEnd: 998287
      name: 3274
     score: 0
    strand: +
thickStart: 10376
  thickEnd: 10376
   itemRgb: 9127187
  landmark: 
   varType: CopyNumber
 reference: Redon et al. (2006)
  pubMedId: 17122850
    method: BAC Array CGH
    sample: 270 control samples (HapMap)
*************************** 2. row ***************************
       bin: 73
     chrom: chr1
chromStart: 10498
  chromEnd: 177368
      name: 68173
     score: 0
    strand: +
thickStart: 10498
  thickEnd: 10498
   itemRgb: 200
  landmark: 
   varType: CopyNumber
 reference: Conrad et al. (2009)
  pubMedId: 19812545
    method: NimbleGen custom 42M oligo array CGH
    sample: 39 HapMap Individuals + NA15510

[khikho]

Thanks Pierre But how can I get whole list of Tables and their fields?!

[Pierre Lindenbaum]

use the UCSC table browser and select "describe table schema"