{"id":1288,"date":"2020-04-06T00:10:16","date_gmt":"2020-04-05T15:10:16","guid":{"rendered":"http:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1288"},"modified":"2020-04-06T00:10:42","modified_gmt":"2020-04-05T15:10:42","slug":"single-end-read%e3%81%ae%e3%83%87%e3%83%bc%e3%82%bf%e3%82%92pair-end%e3%81%ab%e3%81%99%e3%82%8b%e3%80%82","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1288","title":{"rendered":"[bioinfo]Single-end read\u306e\u30c7\u30fc\u30bf\u3092Pair-end\u306b\u3059\u308b\u3002"},"content":{"rendered":"\n<p><strong><a href=\"https:\/\/github.com\/BioInfoTools\/BBMap\">BBMap<\/a><\/strong>\u306ebbfakereads.sh\u3092\u5229\u7528\u3059\u308b\u3002<\/p>\n\n\n\n<p>BBMap\u306e\u30a4\u30f3\u30b9\u30b3\u3002conda\u3067\u5373\u3002<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">conda install -c bioconda bbmap<\/pre>\n\n\n\n<p>bbfakereads\u306f\u7d76\u5bfe\u30d1\u30b9\u3092\u6253\u3061\u8fbc\u3093\u3067\u4f7f\u3046\u3002\u81ea\u5206\u306e\u30db\u30fc\u30e0\u30d5\u30a9\u30eb\u30c0\u306bminiconda\u3092\u30a4\u30f3\u30b9\u30b3\u3057\u3066\u3044\u308b\u5834\u5408\u306f\u3001\/home\/username\/miniconda3\/bin\/bbfakereads.sh<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">>\/home\/username\/miniconda3\/bin\/bbfakereads.sh\n\nWritten by Brian Bushnell\nLast modified February 17, 2015\nDescription: Generates fake read pairs from ends of contigs or single reads.\nUsage: bbfakereads.sh in= out= out2=\nOut2 is optional; if there is only one output file, it will be written interleaved.\nStandard parameters:\now=f (overwrite) Overwrites files that already exist.\nzl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).\nfastawrap=100 Length of lines in fasta output.\ntuc=f (touppercase) Change lowercase letters in reads to uppercase.\nqin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.\nqout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).\nqfin=&lt;.qual file> Read qualities from this qual file, for the reads coming from 'in='\nqfout=&lt;.qual file> Write qualities from this qual file, for the reads going to 'out='\nqfout2=&lt;.qual file> Write qualities from this qual file, for the reads coming from 'out2='\nverifyinterleaved=f (vint) When true, checks a file to see if the names look paired. Prints an error message if not.\ntossbrokenreads=f (tbr) Discard reads that have different numbers of bases and qualities. By default this will be detected and cause a crash.\nFaking parameters:\nlength=250 Generate reads of this length.\nminlength=1 Don't generate reads shorter than this.\noverlap=0 If you set overlap, then reads will by variable length, overlapping by 'overlap' in the middle.\nidentifier=null (id) Output read names are prefixed with this.\naddspace=t Set to false to omit the space before \/1 and \/2 of paired reads.\nJava Parameters:\n-Xmx This will set Java's memory usage, overriding autodetection.\n-Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.\nThe max is typically 85% of physical memory.\n-eoom This flag will cause the process to exit if an\nout-of-memory exception occurs. Requires Java 8u92+.\n-da Disable assertions.\nPlease contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.<\/pre>\n\n\n\n<p>\u4ee5\u4e0b\u306f\u5b9f\u884c\u4f8b\u3002400bp\u306eSE read\u309250bp\u88ab\u3089\u305b\u3066PE read\u3068\u3057\u3066\u51fa\u529b\u3002<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">bbfakereads.sh -Xmx100g in=input.fastq.gz out1=output1.fq out2=output2.fq length=250 ow=t<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>BBMap\u306ebbfakereads.sh<\/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":"http:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1288","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1288","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\/1288","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=1288"}],"version-history":[{"count":2,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1288\/revisions"}],"predecessor-version":[{"id":1290,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1288\/revisions\/1290"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1288"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1288"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1288"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}