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KeyError: "None of [Int64Index ... in wgdi -c

7

Hi there, I'm facing the error below when running the "wgdi -c " command I'm using Ptrichocarpa from Phytozome blockinfo = Ptrichocarpa_Ptrichocarpa.blockinfo.csv lens1 = Ptrichocarpa.lens lens2 = Ptrichocarpa.lens tandem =...

amvarani

关于祖先核型构建的几个疑问

2

孙老师您好！我有几个疑问. 1. 首先只用一个物种T. sinense(tsi)得到了第一个祖先核型即AEK, 植物存在WGD, 所以一堆WGD产生的染色体选一条即可. 2. 但如果是不存在WGD的动物, 原始的lens.file就等于老师用到的aek_tsi13s.txt(WGD产生的多条同源染色体中选一条)吗？ 3. 再接着运行-d -icl -bi -c -km, 最后再画一个点图, 初步的流程就跑通了; 老师在github中提到"We used V. vinifera to validate this AEK result", 用第二个物种V. vinifera(vvi)验证AEK的结果; (dotplot/vvi161s_aek_tsi13s) 该路径下total.conf中"ancestor_left...

kuangzhuoran

deal_gff.py improvement

1

Hello SunPeng Can we change the python deal_gff.py in a way that can sort the genome file and gff file in descending order (based on the length of chromosomes in...

ardy20

Ancestor is unknown

11

Hi SunPeng What is the best approach when the ancestor is unknown and there is no information about ancestor of testing plant species? Regards

ardy20