Dear Pasi Rastas,
I try to contruct genetic map of apple tree (CP population).and I really can not understand how to construct two map(femal and male) genetic map just like Joinmap, I try my best and I can get consensus map only. I want to ask 1) can the Lep-map2 be used to contruct genetic map of trees （CP poplulation ) 2) can the software generate two map or just consensus map.
Best
Flynn Shen
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LM outputs two map positions for each marker, paternal and maternal. If this is not what you want, you can filter out markers based on their informativeness, using informativeMask (eg. 1 or 2). Then the non-informative sex has map position 0.
Cheers,
Pasi
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Thanks for your response，I constructed a genetic map. but I find the genetic map is unexpected long. Can you give me some suggestions or options to solve this problem?
Best,
Flynn Shen
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It is hard to say why the maps are too long without seeing the data. Oftern this is due to problems with the data. If you trust that all the individuals are correct then you could use more stringent filtering on the data to see if it makes a difference in the map lengths.
Also typically the map lengths are right if you have about as many markers per chromosome as you have individuals. Finally, note that erronous markers tend to cluster at map ends and can cause long gaps (hence inflate map lengths)
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Pasi Rastas,
I try to contruct genetic map of apple tree (CP population).and I really can not understand how to construct two map(femal and male) genetic map just like Joinmap, I try my best and I can get consensus map only. I want to ask 1) can the Lep-map2 be used to contruct genetic map of trees （CP poplulation ) 2) can the software generate two map or just consensus map.
Best
Flynn Shen
Dear Flynn Shen,
Thank you for your email.
LM outputs two map positions for each marker, paternal and maternal. If this is not what you want, you can filter out markers based on their informativeness, using informativeMask (eg. 1 or 2). Then the non-informative sex has map position 0.
Cheers,
Pasi
Dear Pasi Rastas,
Thanks for your response，I constructed a genetic map. but I find the genetic map is unexpected long. Can you give me some suggestions or options to solve this problem?
Best,
Flynn Shen
Dear Shenfei,
Thank you for your question.
It is hard to say why the maps are too long without seeing the data. Oftern this is due to problems with the data. If you trust that all the individuals are correct then you could use more stringent filtering on the data to see if it makes a difference in the map lengths.
Also typically the map lengths are right if you have about as many markers per chromosome as you have individuals. Finally, note that erronous markers tend to cluster at map ends and can cause long gaps (hence inflate map lengths)
Cheers,
Pasi