huangl07 / bioinformatics Goto Github PK
View Code? Open in Web Editor NEWtools for biolinux
License: GNU General Public License v3.0
tools for biolinux
License: GNU General Public License v3.0
你好,
在开发遗传图谱流程的过程中,看了一下您这里代码,我觉得有两个问题可以探讨一下
1)参考基因组比较好的物种,如水稻、玉米、大豆等没有必要重新排图,直接按物理位置校正基因型后计算遗传距离即可,从头排图还会带了后期qtl定位结果注释困难的问题。如下几篇文献就是这么做的,
https://genome.cshlp.org/content/19/6/1068
https://www.pnas.org/content/107/23/10578
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-433
https://doi.org/10.1016/j.molp.2017.03.006
只有在需要对基因进行优化或者亲本与参考差异比较大的时候需要按无参的方式进行排图。
2)这个流程里的binmap得出的结果可能不符合遗传图中bin的实际定义,也就是取完bin以后从头排图可能出现遗传位置一样的两个或多个bin标记,遗传图中bin是针对遗传位置唯一性进行定义的。
我是想针对有染色体水平参考的物种,直接按照上面这些文献的方法去做。不知我的说法有什么不妥之处。
Best wishes
谢坤
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