Month: June 2021
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ViewBS:DNA甲基化数据的可视化
官网提供了三种安装方式:conda、docker和正常一步步安装,前两种较为简单,能解决较多的依赖关系,下边介绍一步步安装(https://github.com/xie186/ViewBS) #安装htslib git clone https://github.com/samtools/htslib.git git submodule update –init –recursive autoreconf ./configure make sudo make insatll #安装ViewBS wget -c https://github.com/xie186/ViewBS/archive/refs/tags/v0.1.10.tar.gz tar -zxvf v0.1.10.tar.gz cd ViewBS-0.1.10 /opt/biosoft/ViewBS-0.1.10/ext_tools/cpanm –local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib) /opt/biosoft/ViewBS-0.1.10/ext_tools/cpanm Getopt::Long::Subcommand /opt/biosoft/ViewBS-0.1.10/ext_tools/cpanm Getopt::Long (> 2.50) /opt/biosoft/ViewBS-0.1.10/ext_tools/cpanm –force Bio::DB::HTS::Tabix ViewBS主要以Bismark的bismark_methylation_extractor输出结果为输入,同时根据不同的目的需要准备全基因组DNA序列的fasta文件,所有基因的bed文件,转座子bed文件,差异基因的bed文件等。 #数据准备 samtools faidx genome.fasta bgzip ../A.1_bismark_bt2_pe.deduplicated.CX_report.txt ./ #Bismark结果需要bgzip压缩 tabix -p vcf…