{"id":2395,"date":"2015-11-17T02:05:45","date_gmt":"2015-11-16T18:05:45","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2395"},"modified":"2015-11-17T02:06:01","modified_gmt":"2015-11-16T18:06:01","slug":"human-genome-h38-infromation-downloading","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2395","title":{"rendered":"human genome h38 infromation downloading"},"content":{"rendered":"<p>Writing date: 2015-11-17.<\/p>\n<p>The latest Human Genome assembly version is : GRCh38 (GCA_000001405.15) . GRch38: Genome Reference Consortium Human Reference 38.<\/p>\n<p>The GRch38 genome browses:<br \/>\nUCSC\thttp:\/\/genome.ucsc.edu\/cgi-bin\/hgGateway<br \/>\nEnsembl\thttp:\/\/www.ensembl.org\/Homo_sapiens\/Info\/Index<br \/>\nVega\thttp:\/\/vega.sanger.ac.uk\/Homo_sapiens\/Info\/Index<br \/>\nGENCODE\thttp:\/\/www.gencodegenes.org\/human_biodalliance.html<\/p>\n<p>The downloading website of GRch38 information in Ensembl: http:\/\/www.ensembl.org\/info\/data\/ftp\/index.html<br \/>\nI recommend to download gh38 sequence functional annotations from Ensembl: ftp:\/\/ftp.ensembl.org\/pub\/release-82\/genbank\/homo_sapiens\/.<\/p>\n<pre>\r\nmdkir sequence_annotation\r\ncd sequence_annotation\r\nlftp -e \"mirror -c --parallel=5 \/pub\/release-82\/genbank\/homo_sapiens\/\" ftp:\/\/ftp.ensembl.org\r\ncd ..\r\n<\/pre>\n<p>The downloading website of GRch38 information in GENCODE: http:\/\/www.gencodegenes.org\/releases\/23.html<br \/>\nI recommend to download gh38 fasta and gff3 files from GENCODE. These 2 files would be the main fasta and gff3 files for most users.<\/p>\n<pre>\r\nwget ftp:\/\/ftp.sanger.ac.uk\/pub\/gencode\/Gencode_human\/release_23\/GRCh38.primary_assembly.genome.fa.gz\r\nwget ftp:\/\/ftp.sanger.ac.uk\/pub\/gencode\/Gencode_human\/release_23\/gencode.v23.basic.annotation.gff3.gz\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>Writing date: 2015-11-17. The latest Hum &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2395\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2395"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2395"}],"version-history":[{"count":2,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2395\/revisions"}],"predecessor-version":[{"id":2397,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2395\/revisions\/2397"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2395"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2395"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2395"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}