{"id":2217,"date":"2023-03-30T12:23:08","date_gmt":"2023-03-30T03:23:08","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=2217"},"modified":"2023-03-31T22:48:43","modified_gmt":"2023-03-31T13:48:43","slug":"bioinfobraken%e3%82%92%e4%bd%bf%e3%81%a3%e3%81%a6kraken2%e3%81%ae%e7%b5%90%e6%9e%9c%e3%81%ab%e3%81%a4%e3%81%84%e3%81%a6%e9%87%8f%e7%9a%84%e3%81%aa%e8%a7%a3%e6%9e%90%e3%82%92%e8%a1%8c%e3%81%86","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=2217","title":{"rendered":"[bioinfo]braken\u3092\u4f7f\u3063\u3066kraken2\u306e\u7d50\u679c\u306b\u3064\u3044\u3066\u91cf\u7684\u306a\u89e3\u6790\u3092\u884c\u3046"},"content":{"rendered":"\n

braken\u306f\u3053\u3053<\/a>\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9<\/p>\n\n\n\n

git clone https:\/\/github.com\/jenniferlu717\/Bracken<\/pre>\n\n\n\n
\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3092\u4f5c\u308b\u3002kraken2\u3092\u4f7f\u3063\u3066\u3044\u308b\u5834\u5408\u306f-k 35\u3001\u4eca\u56de\u306f16S\u306e\u307b\u307c\u5168\u9577\u3092\u5897\u3084\u3057\u3066\u3044\u308b\u306e\u3067-l 1500\u3068\u3059\u308b\u3002\u30b3\u30f3\u30b7\u30e5\u30fc\u30de\u30fcPC\uff08Core i7-9800X 3.80GHz x 16, 128Gb RAM\uff09\u3060\u3068\u4e00\u65e5\u4ee5\u4e0a\u6642\u9593\u3092\u8981\u3059\u308b\u3002<\/p>\n\n\n\n
braken-build -d \/where\/karakendb\/installed -t 16 -k 35 -l 1500 -x \/where\/kraken2\/installed<\/pre>\n\n\n\n
braken\u3092\u4f7f\u3063\u3066kraken2\u306e\u7d50\u679c\u3092\u88dc\u6b63\u3059\u308b\u3002
-d kraken\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306e\u5834\u6240
-i kraken\u306e\u30ec\u30dd\u30fc\u30c8\u30d5\u30a1\u30a4\u30eb
-l \u5206\u985e\u30ec\u30d9\u30eb\u306e\u6307\u5b9a [Default = ‘S’ (\u7a2especies)\u3001’D’ (\u30c9\u30e1\u30a4\u30f3domain)\u3001’P’ (\u9580phylum)\u3001’C’ (\u7db1class\uff09\u3001’O’ (\u76eeorder)\u3001’F’ (\u79d1family)\u3001’G’ (\u5c5egenus)\u3001’S’ (\u7a2especies)]
-o braken\u306eoutput\u30d5\u30a1\u30a4\u30eb\u540d
-r read\u9577\u306e\u6307\u5b9a\uff08\u4eca\u56de\u306fnanopore data\u306a\u306e\u3067\u30011500bp\uff09
-t threshold (minimum \u30ea\u30fc\u30c9\u6570\uff09<\/p>\n\n\n\n
bracken -d krackendb -i kraken2.report -l P -o bracken.out -r 1500 -t 5<\/pre>\n\n\n\n
\n\n\n\n
\u51fa\u3066\u304d\u305f\u500b\u5225\u306e\u30b5\u30f3\u30d7\u30eb\u306e\u30c7\u30fc\u30bf\u3092\u4e00\u3064\u306e\u30c6\u30fc\u30d6\u30eb\u306b\u7d50\u5408\u3059\u308b\u3002<\/strong><\/h2>\n\n\n\n
bracken\u306e\u30d1\u30c3\u30b1\u30fc\u30b8\u306b\u3042\u308b\u30b9\u30af\u30ea\u30d7\u30c8\u3067\u7d50\u5408\u3059\u308b\u3002<\/p>\n\n\n\n
python \/Bracken\/analysis_scripts\/combine_bracken_outputs.py --files *bracken.out -o merged<\/pre>\n\n\n\n
taxid = sample_counts[name].keys()[0]
TypeError: ‘dict__keyes’ object isno subscriptable
\u3068\u3044\u3046\u30a8\u30e9\u30fc\u304c\u51fa\u308b\u5834\u5408\u306f\u3001133\u884c\u76ee\u306e<\/p>\n\n\n\n
taxid = sample_counts[name].keys()[0]<\/pre>\n\n\n\n
\u3092<\/p>\n\n\n\n
taxid = list(sample_counts[name].keys())[0]<\/pre>\n\n\n\n
\u306b\u7de8\u96c6\u3059\u308b\u3068\u826f\u3044\u3002<\/p>\n\n\n\n
\n\n\n\n
\u7279\u5b9a\u306etaxon\u306e\u30ea\u30fc\u30c9\u3092\u62bd\u51fa\u3059\u308b\u3002<\/h2>\n\n\n\n
KrakenTools\u306eextract_kraken_reads.py\u3092\u5229\u7528\u3059\u308b\u3002\u8907\u6570\u306b\u6e21\u308bfastq\u30c7\u30fc\u30bf\u306f\u53d7\u3051\u4ed8\u3051\u306a\u3044\uff08\u30da\u30a2\u30a8\u30f3\u30c9\u30c7\u30fc\u30bf\u306fOK\uff09\u3002<\/p>\n\n\n\n
extract_kraken_reads.py -k kraken2_out -s concat.fastq.gz -t 1117 --include-children -o selected.fastq --fastq-output<\/pre>\n","protected":false},"excerpt":{"rendered":"
braken\u306f\u3053\u3053\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9 gi<\/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=2217","footnotes":""},"categories":[7],"tags":[],"class_list":["post-2217","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\/2217","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=2217"}],"version-history":[{"count":4,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/2217\/revisions"}],"predecessor-version":[{"id":2225,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/2217\/revisions\/2225"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2217"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2217"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2217"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}