Replies

• Pierre Lindenbaum

  20 July 2007 | 14:40

  I found such data on the UCSC mysql server (the data is here , but you’ll need to known SQL or ask someone).

  Hope it helps.

  Pierre

  mysql—user=genome—host=genome-mysql.cse.ucsc.edu -A -Dhg18

  mysql> select name,marshfieldChrom,marshfieldPos,decodeChrom,decodePos from stsMap where marshfieldPos>0 or decodePos>0 limit 10\G

  +++++++++++++ 1 row
  name: AFM280WE5
  marshfieldChrom: chr1
  marshfieldPos: 4.22
  decodeChrom: chr1
  decodePos: 4
  +++++++++++++ 2 row
  name: AFM344WE9
  marshfieldChrom: chr1
  marshfieldPos: 8.85
  decodeChrom: chr1
  decodePos: 6.43
  +++++++++++++ 3 row
  name: AFM123XC3
  marshfieldChrom: chr1
  marshfieldPos: 10.78
  decodeChrom: chr1
  decodePos: 6.43
  +++++++++++++ 4 row
  name: AFMA203YC1
  marshfieldChrom: chr1
  marshfieldPos: 10.78
  decodeChrom: chr1
  decodePos: 7.09
  +++++++++++++ 5 row
  name: GATA68D01
  marshfieldChrom: chr1
  marshfieldPos: 10.78
  decodeChrom: chr1
  decodePos: 8.06
  +++++++++++++ 6 row
  name: AFMB355ZH5
  marshfieldChrom: chr1
  marshfieldPos: 11.87
  decodeChrom: 0
  decodePos: 0
  +++++++++++++ 7 row
  name: AFMA131YA5
  marshfieldChrom: chr1
  marshfieldPos: 11.87
  decodeChrom: chr1
  decodePos: 10.11
  +++++++++++++ 8 row
  name: AFMA052WG1
  marshfieldChrom: chr1
  marshfieldPos: 14.04
  decodeChrom: chr1
  decodePos: 11.37
  +++++++++++++ 9 row
  name: AFM254WB9
  marshfieldChrom: chr1
  marshfieldPos: 14.59
  decodeChrom: 0
  decodePos: 0
  +++++++++++++ 10 row
  name: AFMB039ZG9
  marshfieldChrom: chr1
  marshfieldPos: 14.04
  decodeChrom: chr1
  decodePos: 12
  10 rows in set (0,31 sec)

• Pierre Lindenbaum

  20 July 2007 | 14:44

  BTW,
  you can also download this table from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/stsMap.txt.gz

  Pierre

• Lorna Houlihan

  24 July 2007 | 10:48

  Thank you. However, it looks like some of my microsatellite markers do not have any DeCODE co-ordinates. Do you know if there is a way to extrapolate Marshfield co-ordinates to DeCODE co-ordinates?
  Many thanks,
  Lorna

• Claire Simpson

  25 July 2007 | 15:27

  If you have flanking markers which are on the DeCode Map, you could use those to translate the DeCode map onto the Marshfield map. It won’t be very accurate doing it this way, but I guess it’s better than nothing.

  So if you data looks like the following:

  Marker DeCode Map Marshfield Map
  Marker1 5 7
  Marker2 5.5 7.4
  Marker3 7.9
  Marker4 6 8.3

  Calculate the Decode units per Marshfield unit for each marker and then use a mean of that value multiplied by the Marshfield position will give you an approximate location for your marker. Does that make sense?
  Cheers,

  Claire

• Lorna Houlihan

  25 July 2007 | 15:39

  Thanks Claire. It does make sense. Actually, I ended up using a program called Cartographer and for in-house markers, I used linear interpolation as done by DeCODE to estimate the DeCODE cM genetic distance.
  Thanks for your help, Lorna