{"id":1900,"date":"2022-06-16T16:00:36","date_gmt":"2022-06-16T07:00:36","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1900"},"modified":"2022-06-22T00:30:48","modified_gmt":"2022-06-21T15:30:48","slug":"bioinfo-repeatscout%e3%81%a7%e6%96%b0%e8%a6%8f%e3%82%b2%e3%83%8e%e3%83%a0%e4%b8%ad%e3%81%ae%e3%83%aa%e3%83%94%e3%83%bc%e3%83%88%e9%a0%98%e5%9f%9f%e3%82%92%e5%90%8c%e5%ae%9a%e3%81%99%e3%82%8b","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1900","title":{"rendered":"[bioinfo]RepeatScout\u3067\u65b0\u898f\u30b2\u30ce\u30e0\u4e2d\u306e\u30ea\u30d4\u30fc\u30c8\u9818\u57df\u3092\u540c\u5b9a\u3059\u308b"},"content":{"rendered":"\n

\u65b0\u3057\u3044\u30b2\u30ce\u30e0\u914d\u5217\u306b\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u3092\u4ed8\u3051\u308b\u305f\u3081\u3001\u307e\u305a\u306f\u30b2\u30ce\u30e0\u4e2d\u306b\u6563\u5728\u3059\u308b\u30ea\u30d4\u30fc\u30c8\u9818\u57df\u3092\u30de\u30b9\u30af\u3059\u308b\u3053\u3068\u306b\u3057\u305f\u306e\u3060\u304c\u3001RepBase\u304c\u6709\u6599\u3067\u3042\u308b\u3057\u3001Dfam\u306f\u4e21\u751f\u985e\u306b\u7279\u5316\u3057\u305f\u30c7\u30fc\u30bf\u306f\u306a\u3044\u3088\u3046\u306a\u306e\u3067\u3001\u307e\u305a\u306f\u3069\u3093\u306a\u3082\u306e\u304c\u3042\u308b\u306e\u304b\u3092\u77e5\u308b\u4e0a\u3067\u3082RepeatScout\u3092\u5229\u7528\u3057\u3066\u30ea\u30d4\u30fc\u30c8\u9818\u57df\u3092\u540c\u5b9a\u3057\u3066\u307f\u308b\u3053\u3068\u306b\u3057\u305f\u3002<\/p>\n\n\n\n

RepeatScout
http:\/\/bix.ucsd.edu\/repeatscout\/
https:\/\/github.com\/mmcco\/RepeatScout
\u66f4\u65b0\u306f\u3060\u3044\u3076\u524d\u306b\u6b62\u307e\u3063\u3066\u3044\u308b\u69d8\u5b50\u3002web\u4e0a\u3067\u306fver1.0.5\u304c\u6700\u65b0\u3068\u306a\u3063\u3066\u3044\u308b\u304c\u3001conda\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b\u30681.0.6\u304c\u5165\u308b\u3002
\u4ed6\u306b\u3082Tandem Repeat Finder\u3084nseg\u3082\u5fc5\u8981\u306b\u306a\u308b\u306e\u3067\u3001\u540c\u69d8\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u304a\u304f\u3002<\/p>\n\n\n\n

\u4e0a\u5742\u3055\u3093\u306e\u8a18\u4e8b<\/a>\u3092\u53c2\u8003\u306b\u3057\u305f\u3002
\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u306f\u4e0a\u8a18\u306e\u3088\u3046\u306bconda\u4e00\u629e\u3002<\/p>\n\n\n\n

conda install -c bioconda repeatscout<\/pre>\n\n\n\n
\u67d3\u8272\u4f53\u30ec\u30d9\u30eb\u307e\u3067\u30a2\u30bb\u30f3\u30d6\u30eb\u304c\u9032\u3093\u3067\u3044\u308b\u5834\u5408\u306f\u3001\u67d3\u8272\u4f531\u672c\u3092\u7cbe\u67fb\u3059\u308c\u3070OK\u3089\u3057\u3044\u306e\u3060\u304c\u3001\u3072\u3068\u307e\u305a\u30b2\u30ce\u30e0\u5168\u4f53\u3067\u3084\u3063\u3066\u307f\u308b\u3053\u3068\u306b\u3057\u305f\u3002\u3068\u3053\u308d\u304c\u3001RepeatScout\u306e\u30b9\u30af\u30ea\u30d7\u30c8”build_lmer_table”\u306f\u5927\u304d\u306a\u30d5\u30a1\u30a4\u30eb\u306b\u306f\u5bfe\u5fdc\u3067\u304d\u306a\u3044\u3089\u3057\u304f\u3001memory allocation error\u304c\u51fa\u308b\u3002\u305d\u306e\u305f\u3081\u3001\u307e\u305a\u3001seqkit\u3067\u30b2\u30ce\u30e0\u306efasta\u309210\u500b\u3050\u3089\u3044\u306b\u5207\u308a\u5206\u3051\u3066\u3001\u305d\u306e\u3042\u3068\u306bbuild_lmer_table\u3092\u884c\u3063\u305f\u3002<\/p>\n\n\n\n
seqkit split -p 10 genome.fasta\nfor i in 001 002 003 004 005 006 007 008 009 010 ; do build_lmer_table -l 14 -sequence genome.fasta.split\/genome.part.$i.fasta -freq lmer_table$i ; done<\/pre>\n\n\n\n
RepeatScout\u3067\u30ea\u30d4\u30fc\u30c8\u30c6\u30fc\u30d6\u30eb\u304b\u3089FASTA\u3092\u751f\u6210\u3059\u308b\u3002<\/p>\n\n\n\n
for i in 001 002 003 004 005 006 007 008 009 010 ; do RepeatScout -sequence genome.fasta.split\/genome.part.$i.fasta -output out_repeats$i.fasta -freq lmer_table$i -l 14 ; done<\/pre>\n\n\n\n
filter-stage-1.prl\u3092\u4f7f\u3063\u3066\u3001\u5358\u7d14\u30ea\u30d4\u30fc\u30c8\u3068\u7e70\u308a\u8fd4\u3057\u657010\u4ee5\u4e0b\u306e\u30ea\u30d4\u30fc\u30c8\u3092\u6392\u9664\u3059\u308b\u3002<\/p>\n\n\n\n
for i in 001 002 003 004 005 006 007 008 009 010 ; do cat out_repeats$i.fasta | filter-stage-1.prl > repeats_filtered_stg1_$i.fasta ; done<\/pre>\n\n\n\n
RepeatMasker\u3067\u30d5\u30a3\u30eb\u30bf\u30ea\u30f3\u30b0\u3055\u308c\u305f\u9818\u57df\u3092\u5206\u6790\u3057\u306a\u304c\u3089\u3001\u898f\u7a0b\u56de\u6570\uff083\u56de\u4ee5\u4e0a\uff09\u767b\u5834\u3057\u306a\u304b\u3063\u305f\u30ea\u30d4\u30fc\u30c8\u3092\u6392\u9664\u3059\u308b\u3002\u3053\u306e\u3068\u304d\u3001fasta\u306eID\u304c50\u6587\u5b57\u4ee5\u4e0a\u3060\u3068\u52d5\u304b\u306a\u3044\u306e\u3067sed\u306a\u3069\u3067\u77ed\u304f\u3059\u308b\u3002<\/p>\n\n\n\n
RepeatMasker -pa 20 -s -lib repeats_filtered_stg1.fasta genome.fasta & cat repeats_filtered_stg1.fasta | filter-stage-2.prl --cat=final_assembly.fasta.out --thresh=3 > repeats_filtered_stg2.fasta<\/pre>\n\n\n\n
\uff08\u7d9a\u304f\uff09<\/p>\n","protected":false},"excerpt":{"rendered":"
\u65b0\u3057\u3044\u30b2\u30ce\u30e0\u914d\u5217\u306b\u30a2\u30ce\u30c6\u30fc\u30b7\u30e7\u30f3\u3092\u4ed8\u3051\u308b<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"colormag_page_container_layout":"default_layout","colormag_page_sidebar_layout":"default_layout","_locale":"ja","_original_post":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1900","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1900","post","type-post","status-publish","format-standard","hentry","category-protocol","ja"],"_links":{"self":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1900","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1900"}],"version-history":[{"count":8,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1900\/revisions"}],"predecessor-version":[{"id":1920,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1900\/revisions\/1920"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1900"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1900"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1900"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}