For SNPs, we set the thresholds as −log10(P value) = 6, 6, and 4 for litter size, numbers of horns and nipples, respectively.
请问，这种自选的阈值，怎么选择呢？为什么有的是6有的是4呢？
在采用TCGAbiolinks 下载TCGA数据时，有时候会出现“Error in value[[3L]](cond) : GDC server down, try to use this package later”的错误。
这个错误一般不会出现，除非GDC的网站有问题，检测方法有两种：
1. 在R中运行如下命令：
> Genom...
...onfiguration files work, create the example image, whose
configuration and data are found in example/. From the Circos distribution
directory,
cd example
../bin/circos -conf ./circos.conf
or use the 'run' script (UNIX only).
Configuration files are describ...
...e = $im->colorAllocate(0,0,255);
# make the background transparent andinterlaced
$im->transparent($white);
$im->interlaced('true');
# Put a black frame around the picture
$im->rectangle(0,0,99,99,$black);
# Draw a blue oval
$im->arc(50,50,95,75,0,360,$blue);
#...
运行动植物泛基因组教程02.gene_family.sh命令如下：orthofinder.py -f pep \
-S diamond \
-M msa \
-A muscle \
-T fasttree \
-t 10 \
-a 2 报错如下：Best outgroup(s) for species tree---------------------------------2024-11-15 10:50:56 : Starting STRIDEERROR: Species tree inf...