{"id":481,"date":"2020-04-08T22:59:49","date_gmt":"2020-04-08T14:59:49","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=481"},"modified":"2020-04-12T15:00:29","modified_gmt":"2020-04-12T07:00:29","slug":"hic-pro%e8%be%85%e5%8a%a9%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%bb%84%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=481","title":{"rendered":"HiC-pro\u5b89\u88c5\u4e0e\u4f7f\u7528"},"content":{"rendered":"<p>\u8f6f\u4ef6\u5b89\u88c5<\/p>\n<pre>#conda \u5b89\u88c5\u8f6f\u4ef6\u9700\u8981\u7684\u73af\u5883<br \/>\n. ~\/miniconda3\/bin\/activate<br \/>\nconda create -y -n hic-pro python=2.7 pysam bx-python numpy scipy samtools bowtie2<br \/>\nconda activate hic-pro<br \/>\n#\u5b89\u88c5HiC-pro<br \/>\ncd \/opt\/biosoft\/<br \/>\nwget https:\/\/github.com\/nservant\/HiC-Pro\/archive\/v2.11.1.tar.gz<br \/>\ntar -zxvf v2.11.1.tar.gz<br \/>\ncd HiC-Pro-2.11.1<br \/>\nmake<br \/>\nmake install<br \/>\nrm v2.11.1.tar.gz<br \/>\n#\u8f6f\u4ef6\u4f7f\u7528\uff08\u751f\u6210\u8f6f\u4ef6\u8f93\u5165\u9700\u8981\u7684\u4e09\u4e2a\u6587\u4ef6\uff09<br \/>\n\/opt\/biosoft\/HiC-Pro-2.11.1\/bin\/utils\/digest_genome.py -r mboi -o mboi_genome.bed genome.fasta<br \/>\nsamtools faidx genome.fasta<br \/>\nawk '{print $1\"\\t\"$2}' genome.fasta.fai &gt; genome.size<br \/>\nbowtie2-build --threads 140 genome.fasta grass_genome<\/p>\n<p>#\u914d\u7f6e\u6587\u4ef6\u4fee\u6539\u53c2\u8003\u5176\u4ed6\u6559\u7a0b\uff0c\u8f93\u5165\u6587\u4ef6\u586b\u5199\u7edd\u5bf9\u8def\u5f84\uff01<\/p>\n<p>#\u8fd0\u884cHiC-pro<br \/>\nnohup HiC-Pro --input \/home\/wuchangsong\/gc_genome\/10.HIC\/raw_data\/ --output hic_results --conf \/home\/wuchangsong\/gc_genome\/10.HIC\/config-hicpro.txt &<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u8f6f\u4ef6\u5b89\u88c5 #conda \u5b89\u88c5\u8f6f\u4ef6\u9700\u8981\u7684\u73af\u5883 . ~\/miniconda3\/bin\/activate conda create -y -n hic-pro python=2.7 pysam bx-python numpy scipy samtools bowtie2 conda activate hic-pro #\u5b89\u88c5HiC-pro cd \/opt\/biosoft\/ wget https:\/\/github.com\/nservant\/HiC-Pro\/archive\/v2.11.1.tar.gz tar -zxvf v2.11.1.tar.gz cd HiC-Pro-2.11.1 make make install rm v2.11.1.tar.gz #\u8f6f\u4ef6\u4f7f\u7528\uff08\u751f\u6210\u8f6f\u4ef6\u8f93\u5165\u9700\u8981\u7684\u4e09\u4e2a\u6587\u4ef6\uff09 \/opt\/biosoft\/HiC-Pro-2.11.1\/bin\/utils\/digest_genome.py -r mboi -o mboi_genome.bed genome.fasta samtools faidx genome.fasta awk &#8216;{print $1&#8243;\\t&#8221;$2}&#8217; genome.fasta.fai &gt; genome.size bowtie2-build &#8211;threads 140 genome.fasta [&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],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/481"}],"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=481"}],"version-history":[{"count":3,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/481\/revisions"}],"predecessor-version":[{"id":484,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/481\/revisions\/484"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=481"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=481"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=481"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}