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 A.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz #生成tbi结尾的index文件
#分析流程
ViewBS MethCoverage --reference /home/wuchangsong/gc_genome/17.Geta/0.initial_data/genome.fasta --sample A.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Control-1 --sample B.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Control-2 --sample C.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Control-3 --sample D.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Single-1 --sample E.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Single-2 --sample F.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Single-3 --sample G.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Multiple-1 --sample H.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Multiple-2 --sample I.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Multiple-3 --outdir MethCoverage --prefix BS_seq_allsam
ViewBS MethGeno --genomeLength /home/wuchangsong/gc_genome/17.Geta/0.initial_data/genome.fasta.fai --sample A.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Control-1 --sample B.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Control-2 --sample C.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Control-3 --sample D.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Single-1 --sample E.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Single-2 --sample F.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Single-3 --sample G.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Multiple-1 --sample H.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Multiple-2 --sample I.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Multiple-3 --prefix BS_geno_sample --context CG --outdir MethGeno_100k --minLength 1000000 --win 100000 --step 100000
ViewBS MethOverRegion --region repeats.bed --sample A.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Control-1 --sample B.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Control-2 --sample C.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Control-3 --sample D.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Single-1 --sample E.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Single-2 --sample F.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Single-3 --sample G.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Multiple-1 --sample H.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Multiple-2 --sample I.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz,Multiple-3 --prefix bis_gene_all_sample --context CG --outdir MethOverRegion

详细流程参考官网