cnxiaobo94

Hi, I wanna assemble a genome of moose (about 2.7 GB). After filtering reads, I run this command several times with different threads as below, but the same issue occurred...

How to plot multiple boostrap results in one image?

5

Hi, I run psmc on three species with bootstrapping mode (10 times) and generate three results separately. (eg. 1_bootstrap.psmc, 2_bootstrap.psmc, 3_bootstrap.psmc) My question is how to plot these in one...

About the selection of reference genome

1

Hi, dear friends. I have a question on processing rawdata. When I made PCA or Dst. analyses, I need to take a outgroup species as reference genome for processing rawdata....

the command line can not be run with "nohup"

1

[laixl@L001 MSMC2]$ nohup bcftools mpileup -Ou -r CM035273.1 -f ../../../refgenomes/xbinewg/GCA_020226075.1_Hydropotes_inermis_genomic.fa AS_N1.bam --threads 16 | bcftools call -c --threads 16 -V indels | ../../../MSMC2/msmc-tools/bamCaller.py 12 AS_N1_chr5_mask.bed.gz > AS_N1_chr5.vcf & [3] 100129...

Population selections

5

Hi, I'm doing some population demographical analysis among three populations, and I have two questions I'd like to ask for help. 1. There is only one individual in population A,...

installation error

6

Hi, I met a problem with installation of msmc2. Before this installation, DMD and gsl have been installed correctly, and the path of gsl also has been added to makefile...

about RCCR value > 1

2

Dear @stschiff, I have a dataset that consists of three populations as (pop1, (pop2, pop3)). After running msmc2, I have three paired RCCR values, but I met some problems when...

test模式使用

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张老师您好，请问一下，我先做了7个亚种的分析，然后能否用test模式对其中一些拓扑结构进行测试？我用test模式出了错误提示，不知道是我对这个模式理解有误还是有其他问题。 >>>phytop moose_phytop8_50kb_ASTRAL -figsize 4 -colors "#335C81,#A8DADC,#5F9EA0" -test Outgroup,European,Ussuri,Yakutia -outgroup Outgroup -pre moose_phytop8_EU_AS_50kb_ASTRAL 25-11-07 11:37:50 [INFO] No DRMAA (see https://github.com/pygridtools/drmaa-python), Switching to local mode. 25-11-07 11:37:51 [INFO] Command: /home/xiaobo/miniconda3/envs/phytop2/bin/phytop moose_phytop8_50kb_ASTRAL...

Reference genome bias

3

Hello, First of all, I would like to thank you for your work. This software is very convenient. Recently, I have been using Phytop to conduct some analyses, but I...