{"id":783,"date":"2021-06-15T10:08:08","date_gmt":"2021-06-15T02:08:08","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=783"},"modified":"2021-06-15T10:11:49","modified_gmt":"2021-06-15T02:11:49","slug":"viewbsdna%e7%94%b2%e5%9f%ba%e5%8c%96%e6%95%b0%e6%8d%ae%e7%9a%84%e5%8f%af%e8%a7%86%e5%8c%96","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=783","title":{"rendered":"ViewBS:DNA\u7532\u57fa\u5316\u6570\u636e\u7684\u53ef\u89c6\u5316"},"content":{"rendered":"<p>\u5b98\u7f51\u63d0\u4f9b\u4e86\u4e09\u79cd\u5b89\u88c5\u65b9\u5f0f\uff1aconda\u3001docker\u548c\u6b63\u5e38\u4e00\u6b65\u6b65\u5b89\u88c5\uff0c\u524d\u4e24\u79cd\u8f83\u4e3a\u7b80\u5355\uff0c\u80fd\u89e3\u51b3\u8f83\u591a\u7684\u4f9d\u8d56\u5173\u7cfb\uff0c\u4e0b\u8fb9\u4ecb\u7ecd\u4e00\u6b65\u6b65\u5b89\u88c5\uff08https:\/\/github.com\/xie186\/ViewBS\uff09<\/p>\n<pre>#\u5b89\u88c5htslib\ngit clone https:\/\/github.com\/samtools\/htslib.git\ngit submodule update --init --recursive\nautoreconf\n.\/configure\nmake\nsudo make insatll\n#\u5b89\u88c5ViewBS\nwget -c https:\/\/github.com\/xie186\/ViewBS\/archive\/refs\/tags\/v0.1.10.tar.gz\ntar -zxvf v0.1.10.tar.gz\ncd ViewBS-0.1.10\n\/opt\/biosoft\/ViewBS-0.1.10\/ext_tools\/cpanm --local-lib=~\/perl5 local::lib &amp;&amp; eval $(perl -I ~\/perl5\/lib\/perl5\/ -Mlocal::lib)\n\/opt\/biosoft\/ViewBS-0.1.10\/ext_tools\/cpanm Getopt::Long::Subcommand\n\/opt\/biosoft\/ViewBS-0.1.10\/ext_tools\/cpanm Getopt::Long (&gt; 2.50)\n\/opt\/biosoft\/ViewBS-0.1.10\/ext_tools\/cpanm --force Bio::DB::HTS::Tabix\n<\/pre>\n<p>ViewBS\u4e3b\u8981\u4ee5Bismark\u7684bismark_methylation_extractor\u8f93\u51fa\u7ed3\u679c\u4e3a\u8f93\u5165\uff0c\u540c\u65f6\u6839\u636e\u4e0d\u540c\u7684\u76ee\u7684\u9700\u8981\u51c6\u5907\u5168\u57fa\u56e0\u7ec4DNA\u5e8f\u5217\u7684fasta\u6587\u4ef6\uff0c\u6240\u6709\u57fa\u56e0\u7684bed\u6587\u4ef6\uff0c\u8f6c\u5ea7\u5b50bed\u6587\u4ef6\uff0c\u5dee\u5f02\u57fa\u56e0\u7684bed\u6587\u4ef6\u7b49\u3002<\/p>\n<pre>#\u6570\u636e\u51c6\u5907\nsamtools faidx genome.fasta\nbgzip ..\/A.1_bismark_bt2_pe.deduplicated.CX_report.txt .\/ #Bismark\u7ed3\u679c\u9700\u8981bgzip\u538b\u7f29\ntabix -p vcf A.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz #\u751f\u6210tbi\u7ed3\u5c3e\u7684index\u6587\u4ef6\n#\u5206\u6790\u6d41\u7a0b\nViewBS 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\nViewBS 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\nViewBS 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\n<\/pre>\n<p>\u8be6\u7ec6\u6d41\u7a0b\u53c2\u8003<a href=\"https:\/\/github.com\/xie186\/ViewBS\">\u5b98\u7f51<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5b98\u7f51\u63d0\u4f9b\u4e86\u4e09\u79cd\u5b89\u88c5\u65b9\u5f0f\uff1aconda\u3001docker\u548c\u6b63\u5e38\u4e00\u6b65\u6b65\u5b89\u88c5\uff0c\u524d\u4e24\u79cd\u8f83\u4e3a\u7b80\u5355\uff0c\u80fd\u89e3\u51b3\u8f83\u591a\u7684\u4f9d\u8d56\u5173\u7cfb\uff0c\u4e0b\u8fb9\u4ecb\u7ecd\u4e00\u6b65\u6b65\u5b89\u88c5\uff08https:\/\/github.com\/xie186\/ViewBS\uff09 #\u5b89\u88c5htslib git clone https:\/\/github.com\/samtools\/htslib.git git submodule update &#8211;init &#8211;recursive autoreconf .\/configure make sudo make insatll #\u5b89\u88c5ViewBS 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 &#8211;local-lib=~\/perl5 local::lib &amp;&amp; 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 (&gt; 2.50) \/opt\/biosoft\/ViewBS-0.1.10\/ext_tools\/cpanm &#8211;force Bio::DB::HTS::Tabix ViewBS\u4e3b\u8981\u4ee5Bismark\u7684bismark_methylation_extractor\u8f93\u51fa\u7ed3\u679c\u4e3a\u8f93\u5165\uff0c\u540c\u65f6\u6839\u636e\u4e0d\u540c\u7684\u76ee\u7684\u9700\u8981\u51c6\u5907\u5168\u57fa\u56e0\u7ec4DNA\u5e8f\u5217\u7684fasta\u6587\u4ef6\uff0c\u6240\u6709\u57fa\u56e0\u7684bed\u6587\u4ef6\uff0c\u8f6c\u5ea7\u5b50bed\u6587\u4ef6\uff0c\u5dee\u5f02\u57fa\u56e0\u7684bed\u6587\u4ef6\u7b49\u3002 #\u6570\u636e\u51c6\u5907 samtools faidx genome.fasta bgzip ..\/A.1_bismark_bt2_pe.deduplicated.CX_report.txt .\/ #Bismark\u7ed3\u679c\u9700\u8981bgzip\u538b\u7f29 tabix -p vcf [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,3],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/783"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=783"}],"version-history":[{"count":5,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/783\/revisions"}],"predecessor-version":[{"id":788,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/783\/revisions\/788"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=783"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=783"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=783"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}