I am currently learning to use Lepmap3 and have encountered some issues that I would like to consult with you. After performing SeparateChromosomes2, is it necessary for the number of obtained LGs to exactly match the number of chromosomes in the species and correspond one-to-one? Despite trying numerous LOD , I have not obtained the desired results. If the number of LGs obtained exceeds the number of chromosomes, can I remove the extra LGs and keep only the appropriate LGs for OrderMarkers2? If this is possible, how should I go about removing the extra LGs? Also, how should I handle the situation where one chromosome corresponds to multiple LGs? Looking forward to your guidance on this matter.
Thanks,
Dave
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Typically you end up with many small groups and hopefully desired number of large groups. If you end up collapsing two or more groups, you can re-run SeparateChromosomes2 again with the map parameter giving the previous result (and a higher lodLimit). The collapsed group is most likely the largest (lg=1), but if it is not the parameter lg can be given. The small groups can be removed manually or with the parameter sizeLimit.
Cheers,
Pasi
Last edit: Pasi Rastas 2024-05-22
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello Pasi,
I am currently learning to use Lepmap3 and have encountered some issues that I would like to consult with you. After performing SeparateChromosomes2, is it necessary for the number of obtained LGs to exactly match the number of chromosomes in the species and correspond one-to-one? Despite trying numerous LOD , I have not obtained the desired results. If the number of LGs obtained exceeds the number of chromosomes, can I remove the extra LGs and keep only the appropriate LGs for OrderMarkers2? If this is possible, how should I go about removing the extra LGs? Also, how should I handle the situation where one chromosome corresponds to multiple LGs? Looking forward to your guidance on this matter.
Thanks,
Dave
Dear Dave,
Thank you for your question.
Typically you end up with many small groups and hopefully desired number of large groups. If you end up collapsing two or more groups, you can re-run SeparateChromosomes2 again with the map parameter giving the previous result (and a higher lodLimit). The collapsed group is most likely the largest (lg=1), but if it is not the parameter lg can be given. The small groups can be removed manually or with the parameter sizeLimit.
Cheers,
Pasi
Last edit: Pasi Rastas 2024-05-22