{"id":904,"date":"2024-10-15T10:43:15","date_gmt":"2024-10-15T02:43:15","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=904"},"modified":"2024-10-15T20:30:19","modified_gmt":"2024-10-15T12:30:19","slug":"haphic%e5%9f%ba%e5%9b%a0%e7%bb%84%e6%9f%93%e8%89%b2%e4%bd%93%e6%8c%82%e8%bd%bd","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2024\/10\/15\/haphic%e5%9f%ba%e5%9b%a0%e7%bb%84%e6%9f%93%e8%89%b2%e4%bd%93%e6%8c%82%e8%bd%bd\/","title":{"rendered":"Haphic\u57fa\u56e0\u7ec4\u67d3\u8272\u4f53\u6302\u8f7d"},"content":{"rendered":"\t\t
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\u5355\u500d\u578b\u57fa\u56e0\u7ec4\u6302\u8f7d\u795e\u5668-Haphic<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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1. \u8f6f\u4ef6\u5b98\u7f51<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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https:\/\/github.com\/zengxiaofei\/HapHiC<\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2. \u8f6f\u4ef6\u4e0b\u8f7d<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# \u4e0b\u8f7dHaphic<\/p>

git clone https:\/\/github.com\/zengxiaofei\/HapHiC.git<\/p>

# \u901a\u8fc7conda\u7684yml\u6587\u4ef6\u5b89\u88c5\u4f9d\u8d56\u73af\u5883<\/p>

conda env create -f HapHiC\/conda_env\/environment_py310.yml<\/p>

# \u542f\u52a8Haphic\u73af\u5883<\/p>

conda activate haphic # or: source \/path\/to\/conda\/bin\/activate haphic<\/p>

\u00a0\u68c0\u67e5\u8f6f\u4ef6\u4f9d\u8d56<\/p>

\/path\/to\/HapHiC\/haphic check<\/p>

# \u6d4b\u8bd5\u6253\u5370\u8f6f\u4ef6\u5e2e\u52a9\u4fe1\u606f<\/p>

\/path\/to\/HapHiC\/haphic -h<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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3. \u8f6f\u4ef6\u4f7f\u7528<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\u5c06Hi-C\u6d4b\u5e8f\u6570\u636e\u6bd4\u5bf9\u5230\u7ec4\u88c5\u597d\u7684\u57fa\u56e0\u7ec4\u4e0a\uff0c\u4ee5\u6784\u5efaBAM\u6587\u4ef6<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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# \u6bd4\u5bf9
bwa index asm.fa
bwa mem -5SP -t 28 asm.fa \/path\/to\/read1_fq.gz \/path\/to\/read2_fq.gz | samblaster | samtools view – -@ 14 -S -h -b -F 3340 -o HiC.bam<\/p>\n

# \u901a\u8fc7MAPQ >1 \u548cNM < 3\u7b5b\u9009\u6bd4\u5bf9\u7ed3\u679c
\/path\/to\/HapHiC\/utils\/filter_bam HiC.bam 1 –nm 3 –threads 14 | samtools view – -b -@ 14 -o HiC.filtered.bam<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
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\u8fd0\u884cHaphic pipline<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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\/path\/to\/HapHiC\/haphic pipeline asm.fa HiC.filtered.bam nchrs –RE “AAGCTT” –threads 8<\/p>

# nchr \u6539\u6210\u9884\u4f30\u7684\u67d3\u8272\u4f53\u6811\u6728<\/p>

# –RE \u662f\u9176\u5207\u4f4d\u70b9\u7684\u7c7b\u578b<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
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4. \u8f93\u51fa\u7ed3\u679c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
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01.cluster\/corrected_asm.fa<\/b>\uff1a\u66f4\u6b63\u540e\u7684 FASTA \u683c\u5f0f\u7684\u7a0b\u5e8f\u96c6\u3002\u4ec5\u5728\u542f\u7528\u88c5\u914d\u4f53\u6821\u6b63\u65f6\u751f\u6210\u6b64\u6587\u4ef6\u3002<\/p>

04.build\/scaffolds.agp<\/b>\uff1a\u4e00\u4e2a SALSA \u98ce\u683c\u7684 AGP \u6587\u4ef6\uff0c\u5305\u542b\u6709\u5173 corrected_asm.fa \u4e2d\u6240\u6709\u5e8f\u5217\u7684\u811a\u624b\u67b6\u5206\u914d\u3001\u6392\u5e8f\u548c\u65b9\u5411\u4fe1\u606f\u3002\u5982\u679c\u6709\u4efb\u4f55\u5d4c\u5408\u91cd\u53e0\u7fa4\u88ab HapHiC \u6821\u6b63\uff0c\u635f\u574f\u7684\u91cd\u53e0\u7fa4\u5c06\u88ab\u5206\u914d\u65b0\u7684 ID\u3002\uff08\u540e\u9762\u7684\u6784\u5efa\u6302\u8f7d\u56fe\u548cJuicebox\u53ef\u89c6\u5316\u8c03\u6574\u9700\u8981\u7528\u5230\u7684\u7ed3\u679c\uff09<\/strong><\/p>

04.build\/scaffolds.raw.agp<\/b>\uff1a\u4e00\u4e2a YaHS \u98ce\u683c\u7684 AGP \u6587\u4ef6\uff0c\u5305\u542b\u6709\u5173 asm.fa \u4e2d\u6240\u6709\u5e8f\u5217\u7684\u811a\u624b\u67b6\u5206\u914d\u3001\u6392\u5e8f\u548c\u65b9\u5411\u4fe1\u606f\u3002\u4e0d\u4f1a\u4e3a\u65ad\u5f00\u7684\u91cd\u53e0\u7fa4\u5206\u914d\u65b0\u7684 ID\uff0c\u4f46\u5b83\u4eec\u5728\u539f\u59cb\u91cd\u53e0\u7fa4\u4e2d\u7684\u8d77\u59cb\u548c\u7ed3\u675f\u5750\u6807\u5c06\u663e\u793a\u5728\u7b2c\u4e03\u5217\u548c\u7b2c\u516b\u5217\u4e2d\u3002<\/p>

04.build\/scaffolds.fa<\/b>\uff1aFASTA \u683c\u5f0f\u7684\u6700\u7ec8\u811a\u624b\u67b6\u3002\uff08\u67d3\u8272\u4f53\u6302\u8f7d\u540e\u7684scaffold\u6c34\u5e73\u7684\u57fa\u56e0\u7ec4\uff09<\/strong><\/p>

04.build\/juicebox.sh<\/b>\uff1a\u7528\u4e8e Juicebox \u53ef\u89c6\u5316\u548c\u7ba1\u7406\u7684 shell \u811a\u672c\u3002\uff08\u5feb\u901f\u751f\u6210Juicebox\u7684\u8f93\u5165\u6587\u4ef6\u811a\u672c\uff09<\/strong><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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5. \u540e\u7eed\u8865\u5145<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\n\t\t\t\t\t

5.1 \u53ef\u89c6\u5316\u6302\u8f7d\u7ed3\u679c<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
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# \u539f\u59cb\u7684\u6302\u8f7d\u7ed3\u679c<\/p>

\/path\/to\/HapHiC\/haphic plot scaffolds.raw.agp HiC.filtered.bam<\/p>

# \u901a\u8fc7Juicebox\u8c03\u6574\u540e\u7684\u6302\u5728\u7ed3\u679c<\/p>

\/path\/to\/HapHiC\/haphic plot out_JBAT.FINAL.agp HiC.filtered.bam<\/p>

# \u9996\u6b21\u8fd0\u884c\u540e\uff0c\u4f1a\u751f\u6210\u4e00\u4e2acontact_matrix.pkl\uff0c\u8be5\u6587\u4ef6\u53ef\u4ee5\u66ff\u6362\u4e3a.agp\u6587\u4ef6\uff0c\u8ba9plot\u8fd0\u884c\u7684\u8fd0\u884c\u901f\u5ea6\u5f88\u5feb\u3002<\/p>

\/path\/to\/HapHiC\/haphic plot contact_matrix.pkl HiC.filtered.bam<\/span><\/p>

# \u8fd8\u6709\u51e0\u4e2a\u53ef\u4ee5\u8ba9\u7ed3\u679c\u7f8e\u89c2\u7684\u53c2\u6570<\/p>

# –bin_size 1000 \u8bbe\u7f6e\u4e3a\u53ea\u6709\u5927\u4e8e1000bp\u7684scaffold\u624d\u80fd\u663e\u793a\u5728\u56fe\u4e0a\uff0c\u4e00\u822c\u7ecf\u8fc7Juicebox\u8c03\u6574\u540e\uff0c\u4f1a\u6709\u4e00\u4e9b\u5e76\u4e0d\u662f\u67d3\u8272\u4f53\uff0c\u957f\u5ea6\u5f88\u5c0f\u7684scaffold\uff0c\u53ef\u4ee5\u901a\u8fc7\u8fd9\u4e2a\u53c2\u6570\u6765\u8ba9\u8fd9\u4e9bscaffold\u5728\u56fe\u4e0a\u4e0d\u663e\u793a\u3002<\/p>

# –manual_vmax \u70ed\u56fe\u989c\u8272\u7684\u8303\u56f4<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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5.2 Juicebox \u624b\u52a8\u8c03\u6574<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# \u751f\u6210 .hic\u548c.assembly\u6587\u4ef6<\/p>

bash juicebox.sh<\/p>

# \u6839\u636e\u8c03\u6574\u540e\u7684.assembly\u6587\u4ef6\u91cd\u65b0\u751f\u6210.agp\u6587\u4ef6<\/p>

\/path\/to\/HapHiC\/utils\/juicer post -o out_JBAT out_JBAT.review.assembly out_JBAT.liftover.agp asm.fa<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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\u8f93\u51fa\u7ed3\u679c<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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out_JBAT.FINAL.agp<\/b>\uff1a\u8c03\u6574\u540e\u7684agp\u6587\u4ef6<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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5.3 \u4f7f\u7528\u53c2\u8003\u57fa\u56e0\u7ec4\u5bf9Scaffold\u8fdb\u884c\u6392\u5e8f\u548c\u5b9a\u5411<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

\u5728\u5236\u4f5cHIC\u70ed\u56fe\u7684\u65f6\u5019\uff0c\u4e00\u822c\u60c5\u51b5\u4e0b\u90fd\u4f1a\u628a\u5355\u500d\u578b\u7684\u540c\u6e90\u67d3\u8272\u4f53\u653e\u5728\u4e00\u8d77\u5c55\u793a\uff0c\u8fd9\u6837\u770b\u8d77\u6765\u6bd4\u8f83\u76f4\u63a5\u3002Haphic\u53ef\u4ee5\u5c06\u7ec4\u88c5\u597d\u7684\u57fa\u56e0\u7ec4\u901a\u8fc7\u53e6\u5916\u4e00\u4e2a\u8fd1\u7f18\u7269\u79cd\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\uff08\u67d3\u8272\u4f53\u6c34\u5e73\uff09\u8fdb\u884c\u6bd4\u5bf9\uff0c\u4ece\u800c\u5b9e\u73b0\u6392\u5e8f\u548c\u5b9a\u5411\u3002<\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
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# \u6bd4\u5bf9\u5230\u53c2\u8003\u57fa\u56e0\u7ec4<\/p>

minimap2 -x asm20 ref.fa asm.fa –secondary=no -t 28 -o asm_to_ref.paf<\/p>

# \u751f\u6210\u65b0\u7684.agp\u6587\u4ef6\uff08\u6392\u5e8f\u548c\u5b9a\u5411\u540e\uff09<\/p>

haphic refsort 04.build\/scaffolds.raw.agp asm_to_ref.paf > scaffolds.refsort.agp<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t

\n\t\t\t\t\t
\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

\u5355\u500d\u578b\u57fa\u56e0\u7ec4\u6302\u8f7d\u795e\u5668-Haphic 1. \u8f6f\u4ef6\u5b98\u7f51 https:\/\/github.com\/zengxiaofe … \u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":647,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-904","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-6"],"acf":[],"yoast_head":"\nHaphic\u57fa\u56e0\u7ec4\u67d3\u8272\u4f53\u6302\u8f7d - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"description\" content=\"HapHiC \u662f\u4e00\u79cd\u7b49\u4f4d\u57fa\u56e0\u611f\u77e5\u652f\u67b6\u5de5\u5177\uff0c\u5b83\u4f7f\u7528 Hi-C \u6570\u636e\u5c06\u5355\u500d\u578b\u9636\u6bb5\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\u6784\u5efa\u6210\u67d3\u8272\u4f53\u89c4\u6a21\u7684\u5047\u5206\u5b50\u3002\u4e0e\u53e6\u4e00\u79cd\u7b49\u4f4d\u57fa\u56e0\u611f\u77e5\u652f\u67b6 ALLHiC \u4e0d\u540c\uff0cHapHiC \u53ef\u4ee5\u5728\u4e0d\u9700\u8981\u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u60c5\u51b5\u4e0b\u5b9e\u73b0\u8fd9\u4e00\u76ee\u6807\u3002\u6211\u4eec\u7684\u8bc4\u4f30\u8868\u660e\uff0cHapHiC \u7684\u6027\u80fd\u4f18\u4e8e\u5176\u4ed6 Hi-C \u811a\u624b\u67b6\u5de5\u5177\uff0c\u5bf9\u4f4e\u91cd\u53e0\u7fa4 N50 \u7684\u5bb9\u5fcd\u5ea6\u66f4\u9ad8\uff0cHi-C \u6d4b\u5e8f\u6df1\u5ea6\u4f4e\uff0c\u4ee5\u53ca\u5404\u79cd\u7c7b\u578b\u7684\u7ec4\u88c5\u8bef\u5dee\u3002\u6b64\u5916\uff0cHapHiC \u901f\u5ea6\u8d85\u5feb\uff0c\u4e5f\u9002\u7528\u4e8e\u5355\u500d\u578b\u584c\u9677\u7684\u4e8c\u500d\u4f53\u548c\u540c\u79cd\u5f02\u4f53\u591a\u500d\u4f53\u57fa\u56e0\u7ec4\u7ec4\u88c5\u3002\" \/>\n<meta name=\"robots\" content=\"index, follow, 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