{"id":23541,"date":"2024-01-08T17:11:17","date_gmt":"2024-01-08T09:11:17","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23541"},"modified":"2024-01-08T17:11:19","modified_gmt":"2024-01-08T09:11:19","slug":"drlink%e7%9a%84%e5%ae%89%e8%a3%85%e7%ab%9f%e5%a6%82%e6%ad%a4%e7%ae%80%e5%8d%95%ef%bc%9f","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23541","title":{"rendered":"DrLink\u7684\u5b89\u88c5\u7adf\u5982\u6b64\u7b80\u5355\uff1f"},"content":{"rendered":"

\u76f8\u4fe1\u5f88\u591a\u533b\u5b66\u76f8\u5173\u7684\u5de5\u4f5c\u8005\u7ecf\u5e38\u82e6\u607c\u4e8eDrLink\u7684\u5b89\u88c5\uff0c\u56e0\u4e3a\u7f51\u4e0a\u7684\u8d44\u6e90\u5b9e\u5728\u662f\u592a\u5c11\u592a\u5c11\u4e86\uff0c\u9664\u4e86\u4e00\u4e2agithub\u4e3b\u9875\u5c31\u662f\u4e00\u7bc7\u6587\u732e\uff0c\u7ecf\u5e38\u6709\u5c0f\u767d\u5b89\u88c5\u62a5\u9519\u65e0\u4ece\u4e0b\u624b\uff0c\u522b\u62c5\u5fc3\uff0c\u4eca\u5929\u4e00\u7bc7\u6587\u7ae0\u6559\u4f60\u5b66\u4f1a\u3002<\/p>\n

<\/a>DrLink<\/h2>\n

<\/a> \u5b83\u662f\u4e00\u4e2a\u4e0e\u57fa\u56e0\u7ec4\u91cd\u7ec4\u6709\u5173\u7684\u8f6f\u4ef6\uff0c\u5b83\u4f7f\u7528Linked-read\u6d4b\u5e8f\u68c0\u6d4b\u91cd\u7ec4\u65ad\u70b9\u3002\u5b98\u65b9gitHub\u4e2d\u663e\u793a\uff0c\u5b83\u662f\u4e00\u4e2a\u5173\u4e8eDetecting recombination breakpoints using Linked read sequencing\u7684\u8f6f\u4ef6\u3002\u5728\u8fd9\u4e2a\u77ed\u8bed\u4e2d\uff0c\u201cDetecting\u201d\u610f\u5473\u7740\u68c0\u6d4b\u6216\u53d1\u73b0\uff0c\u201crecombination breakpoints\u201d\u6307\u7684\u662f\u57fa\u56e0\u7ec4DNA\u5e8f\u5217\u4e2d\u91cd\u7ec4\u53d1\u751f\u7684\u4f4d\u7f6e\uff0c\u201cLinked-read sequencing\u201d\u662f\u4e00\u79cd\u6d4b\u5e8f\u6280\u672f\uff0c\u5b83\u53ef\u4ee5\u5145\u5206\u5229\u7528\u6761\u5f62\u7801\u6807\u8bb0\u6765\u89e3\u6790\u57fa\u56e0\u7ec4\u533a\u57df\uff0c\u5e76\u66f4\u51c6\u786e\u5730\u786e\u5b9a\u91cd\u7ec4\u65ad\u70b9\u3002\u4e5f\u5c31\u662f\u8bf4\u8be5\u8f6f\u4ef6\u5c31\u662f\u4f7f\u7528Linked-read\u6d4b\u5e8f\u65b9\u6cd5\u6765\u68c0\u6d4b\u57fa\u56e0\u7ec4DNA\u5e8f\u5217\u4e2d\u7684\u91cd\u7ec4\u65ad\u70b9\u3002<\/p>\n

<\/a>\u53c2\u8003\u6587\u732e\uff1a<\/h3>\n

<\/a> DrLink\u662f\u4e00\u4e2a\u751f\u7269\u4fe1\u606f\u5b66\u8f6f\u4ef6\uff0c\u662f\u4e00\u7bc7\u7531Sun\u548cRowan\u7b49\u4eba\u57282019\u5e74\u53d1\u8868\u5728Nature Communications\u4e0a\u7684\u4e00\u7bc7\u8bba\u6587\u6240\u652f\u6301\u7684\u5de5\u5177\u3002\u8be6\u7ec6\u7684\u6e90\u7801\u548c\u7b97\u6cd5\u53ef\u9605\u8bfb\u8be5\u6587\u732e<\/p>\n

Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination<\/a><\/p>\n

<\/a>\u5b89\u88c5\u6b65\u9aa4<\/h3>\n

<\/a>\u5b89\u88c5\u8981\u6c42<\/h4>\n

<\/a> Please refer to INSTALL<\/em> for compiling. The current compilations have been successfully tested on Linux (arch: x_86_64, with g++ version Debian 6.3.0-18+deb9u1 and R<\/em> version 3.5.1).<\/p>\n

<\/a>\u5b89\u88c5\u7684\u8be6\u7ec6\u6b65\u9aa4<\/h4>\n

<\/a> # \u5148\u4ecegithub\u4e0a\u9762\u4e0b\u8f7dDrLink
\ngit clone https:\/\/github.com\/schneebergerlab\/DrLink.git
\n# \u5b89\u88c5\u7684\u547d\u4ee4\u884c
\n# \u8fdb\u5165\u5230\u4f60\u514b\u9686\u7684DrLink\u8f6f\u4ef6\u7684\u8def\u5f84\u4e2d
\ncd \/your_path_to\/DrLink_src
\n# compile gzstream lib (DrLink works with .gz compressed files with the help of gzstream)<\/p>\n

cd gzstream
\nrm libgzstream.a ..\/gzlib\/libgzstream.a<\/p>\n

make clean
\nmake<\/p>\n

cp libgzstream.a ..\/gzlib
\ncd ..<\/p>\n

# compile DrLink<\/p>\n

make
\n# \u914d\u7f6e\u73af\u5883\u53d8\u91cf\uff0c\u8fdb\u800c\u53ef\u5b9e\u73b0\u5168\u5c40\u4f7f\u7528
\nexport PATH=\/media\/desk16\/shb152\/DrLink_src\/:$PATH<\/p>\n

# test<\/p>\n

DrLink
\n# DrLink\u7684usage
\n# which should print the following info<\/p>\n

# Given linked-read sequencing of recombinants, this tool identifies meiotic recombinations.
\n# (version 1.0 – compiled on MM DD YYYY, HH:MM:SS)
\n#
\n# Usage: DrLink subprogram [options]
\n#
\n# Subprograms:
\n# preprocess (Usage: please check options with DrLink preprocess)
\n# molecule (Usage: please check options with DrLink molecule)
\n# recombis (Usage: please check options with DrLink recombis)
\n# intersec (Usage: please check options with DrLink intersec)<\/p>\n

<\/a>\u5b89\u88c5\u65f6\u5e38\u89c1\u7684\u62a5\u9519\uff1a<\/h4>\n
<\/a>Git Clone\u9519\u8bef\uff1a<\/h5>\n

<\/a> GnuTLS recv error (-110): The TLS connection was non-properly terminated.<\/p>\n

<\/a> \u89e3\u51b3\u65b9\u6cd5\uff1a<\/p>\n

<\/a> ubuntu\u7cfb\u7edf\u590d\u5236\u4ee3\u7801\u5373\u53ef\uff0ccentos\u7cfb\u7edf\u628a\u6362\u6210yum install\u5373\u53ef<\/p>\n

<\/a> apt-get install gnutls-bin
\ngit config –global http.sslVerify false
\ngit config –global http.postBuffer 1048576000<\/p>\n

<\/a>\u7f16\u8bd1\u62a5\u9519<\/h4>\n

<\/a> \u5728\u7f16\u8bd1\u65f6\u62a5\u9519\u4e3b\u8981\u539f\u56e0\u5c31\u662f\u6240\u9700\u8981\u7684\u4f9d\u8d56\u6ca1\u6709\u5b89\u88c5\u5b8c\u6bd5\uff0c\u56e0\u6b64\u9700\u8981\u68c0\u67e5\u81ea\u5df1\u7684\u8bbe\u5907\u662f\u5426\u5b89\u88c5\u597d\u4e86\u8be5\u8f6f\u4ef6\u5b89\u88c5\u548c\u8fd0\u884c\u6240\u9700\u8981\u7684\u4f9d\u8d56<\/p>\n

<\/a> The current compilations have been successfully tested on Linux (arch: x_86_64, with g++ version Debian 6.3.0-18+deb9u1 and R<\/em> version 3.5.1).<\/p>\n

<\/a>g++ or gcc\u62a5\u9519<\/h5>\n

<\/a> \u89e3\u51b3\u65b9\u6848\uff1a\u5b89\u88c5\u65b0\u7248gcc\/g++<\/p>\n

<\/a> ##\u521b\u5efa\u865a\u62df\u73af\u5883
\nconda create -n g_test -y
\n#\u63a8\u8350conda\u4e0b\u8f7d\uff0c\u8981\u662f\u51fa\u95ee\u9898\u4e86\uff0c\u63a8\u51fa\u865a\u62df\u73af\u5883\u7136\u540e\u5220\u9664\u8fd9\u4e2aenv\u5373\u53ef
\nconda activate g_test
\nconda install -c conda-forge gcc libgcc
\nconda install -c conda-forge gxx_linux-64
\n# \u8bf7\u66f4\u6362\u4e3a\u81ea\u5df1\u7684\u8def\u5f84
\ncd \/…\/anaconda3\/envs\/…\/bin
\n# \u4f7f\u7528\u8f6f\u94fe\u63a5\u4e5f\u662f\uff0c\u8bf7\u66f4\u6362\u4e3a\u81ea\u5df1\u7684\u8def\u5f84\uff0c\u8fd9\u4e00\u6b65\u7684\u76ee\u7684\u662f\u4e3a\u7684\u5f53\u4f7f\u7528\u547d\u4ee4g++\u7684\u65f6\u5019\u53ef\u4ee5\u7528\u6211\u4eec\u521a\u521a\u5b89\u88c5\u597d\u7684g++
\nln -s \/…\/anaconda3\/envs\/…\/bin\/x86_64-conda_cos6-linux-gnu-g++ g++<\/p>\n

<\/a>\u914d\u7f6e\u73af\u5883\u53d8\u91cf\u76f8\u5173\uff1a<\/h4>\n

<\/a> \u901a\u5e38\u5728\u5176\u4ed6\u8def\u5f84\u8fd0\u884c\u663e\u793a\u6ca1\u6709\u8fd9\u4e2a\u547d\u4ee4\u5c31\u662f\u6ca1\u6709\u914d\u7f6e\u597d\u73af\u5883\u53d8\u91cf<\/p>\n

<\/a>\u5728\u5f53\u524d\u7528\u6237\u7684profile\u4e2d<\/h5>\n

<\/a> \u5728\u5f53\u524d\u7528\u6237\u7684profile\u4e2d\u8bbe\u7f6ePATH
\nvi ~\/.bash_profile
\n# \u4fee\u6539PATH\u884c,\u628a\/usr\/local\/apache\/bin\u6dfb\u52a0\u8fdb\u53bb,\u5982\uff1a
\nPATH=$PATH:$HOME\/bin:\/media\/desk16\/shb152\/DrLink_src\/
\n# \u91cd\u65b0\u52a0\u8f7d\uff0c\u8fdb\u800c\u8ba9\u8fd9\u6b21\u7684\u4fee\u6539\u751f\u6548
\nsource ~\/.bash_profile<\/p>\n

<\/a> \u6ce8\uff1a\u8fd9\u79cd\u65b9\u6cd5\u53ea\u5bf9\u5f53\u524d\u7528\u6237\u8d77\u4f5c\u7528\u7684,\u5176\u4ed6\u7528\u6237\u8be5\u4fee\u6539\u65e0\u6548\u3002<\/p>\n

<\/a>\u5f53\u524d\u4f1a\u8bdd\u914d\u7f6ePATH<\/h5>\n

<\/a> # PATH=$PATH:\/media\/desk16\/shb152\/DrLink_src\/<\/p>\n

<\/a> \u4f7f\u7528\u8fd9\u79cd\u65b9\u6cd5,\u53ea\u5bf9\u5f53\u524d\u4f1a\u8bdd\u6709\u6548\uff0c\u4e5f\u5c31\u662f\u8bf4\u6bcf\u5f53\u767b\u51fa\u6216\u6ce8\u9500\u7cfb\u7edf\u4ee5\u540e\uff0cPATH\u8bbe\u7f6e\u5c31\u4f1a\u5931\u6548\u3002<\/p>\n

<\/a>sudo\u6743\u9650\u53ef\u9009\u62e9\u5728profile\u4e2d\u8bbe\u7f6ePATH\uff0c<\/h5>\n

<\/a> # \u5728profile\u4e2d\u8bbe\u7f6ePATH
\nvi \/etc\/profile
\n# \u627e\u5230export\u884c\uff0c\u5728\u4e0b\u9762\u65b0\u589e\u52a0\u4e00\u884c\uff0c\u5185\u5bb9\u4e3a\uff1a
\nexport PATH=$PATH:\/usr\/local\/apache\/bin
\n# \u5237\u65b0
\nsource profile<\/p>\n

<\/a> \u7f16\u8f91\/etc\/profile\u540ePATH\u7684\u4fee\u6539\u4e0d\u4f1a\u7acb\u9a6c\u751f\u6548\uff0c\u6240\u4ee5\u9700\u8981\u7acb\u5373\u751f\u6548\u7684\u8bdd\uff0c\u53ef\u4ee5\u6267\u884c source profile\u547d\u4ee4\u3002<\/p>\n

<\/a> \u8bf7\u6ce8\u610f\uff1a\u5176\u6b21\u5bf9\u4e8eprofile\u6765\u8bf4\u4e00\u5b9a\u8981\u6ce8\u610f\u6574\u4e2a\u7f16\u8f91\u7684\u8fc7\u7a0b\uff0c\u786e\u4fdd\u8f93\u5165\u683c\u5f0f\u6b63\u786e\uff0c\u5426\u5219\u4e00\u65e6\u4f60\u8f93\u5165\u4e00\u4e9b\u683c\u5f0f\u4e0d\u6b63\u786e\u7684\u6587\u672c\uff08\u5982\u628awindows\u7f16\u7801\u7684\u6587\u672c\u590d\u5236\u8fc7\u6765\uff09\uff0c\u5c31\u4f1a\u9020\u6210profile\u6587\u4ef6\u65e0\u6cd5\u6b63\u5e38\u89e3\u6790\u7b49\u9519\u8bef\u3002<\/a><\/a><\/a><\/a><\/p>\n

\u597d\u5566\uff0c\u901a\u8fc7\u5c0f\u679c\u7684\u4ecb\u7ecd\uff0c\u6709\u6ca1\u6709\u770b\u61c2\u4e86\u5462\uff1f<\/p>\n

\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/p>\n

\u5982\u679c\u60f3\u7528\u670d\u52a1\u5668\u53ef\u4ee5\u8054\u7cfb\u5fae\u4fe1\uff1a18502195490\uff08\u5feb\u6765\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u5427\uff01\uff09<\/p>\n","protected":false},"excerpt":{"rendered":"

\u76f8\u4fe1\u5f88\u591a\u533b\u5b66\u76f8\u5173\u7684\u5de5\u4f5c\u8005\u7ecf\u5e38\u82e6\u607c\u4e8eDrLink\u7684\u5b89\u88c5\uff0c\u56e0\u4e3a\u7f51\u4e0a\u7684\u8d44\u6e90\u5b9e\u5728\u662f\u592a\u5c11\u592a\u5c11\u4e86\uff0c\u9664\u4e86\u4e00\u4e2agithub\u4e3b\u9875 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23541"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=23541"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23541\/revisions"}],"predecessor-version":[{"id":23674,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23541\/revisions\/23674"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23541"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23541"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23541"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}