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MapMan Bugs

RE: soybean Gmax_189 and Gmax_109

soybean Gmax_189 and Gmax_109
Answer
7/24/13 5:34 PM
Hello,

I have tried to use ManMan and found out that maybe the Gmax189 mapping file may have some problem.
When I tried to map my data using Arabidopsis or Gmax109 mapping files were working without any problem, but error message pops up when Gmax189 was selected. I would like to use the Gmax189 rather than Gmax109 since Gmax189 is the recent version.

I would really appreciate if you can check this out.
Thanks very much for your help in advance.

Jin hee

RE: soybean Gmax_189 and Gmax_109
Answer
7/24/13 6:01 PM as a reply to Jin hee Shin.
Hi Jin hee,

i just checked the mapping you referred to (Gmax189) and it loaded and displayed fine in the
MapMan application. So there is no problem in the format or structure of the mapping file itself.

It would be very helpful if you could send me the error message that MapMan issued. I suspect that
the problem is related to the ID format used in the two mapping files. While the Gmax109 mapping file
uses IDs like "glyma02g07180.1", the Gmax189 file was used as obtained from Phytozome where
the corresponding IDs would be "glyma02g07180.1|pacid:26289040". If your data uses the former IDs,
it won't be directly compatible with the Phytozome 9.0 IDs. A simple solution would be either modify the
data file to use the Phytozome 9.0 IDs or to download the Gm189 mapping file in text or excel format,
remove all the "|pacid:26289040"-like sections from the IDs, save it and then import the modified mapping
file into MapMan to use it with your data.

I hope this helps,
best greetings,
Marc

RE: soybean Gmax_189 and Gmax_109
Answer
7/24/13 9:20 PM as a reply to Marc Lohse.
Hello Marc Lohse,

I tried one of your solution: 'download the Gm189 mapping file in text or excel format,
remove all the "|pacid:26289040"-like sections from the IDs, save it and then import the modified mapping
file into MapMan to use it with your data'.

Now it is working perfectly. I really appreciate it!
Thanks very much for your help.

Best wishes,
Jin hee