{"id":72994,"date":"2026-11-15T13:05:18","date_gmt":"2026-11-15T05:05:18","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=72994"},"modified":"2026-11-15T13:07:27","modified_gmt":"2026-11-15T05:07:27","slug":"hisat2-splice-sites-soft-clipping-alignment-rate-practice","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/hisat2-splice-sites-soft-clipping-alignment-rate-practice\/","title":{"rendered":"HISAT2 \u5b9e\u8dd1\u6559\u7a0b\uff5c\u6bd4\u5bf9\u7387\u90fd\u662f 100%\uff0c\u4e3a\u4ec0\u4e48\u526a\u63a5\u7ed3\u679c\u5374\u4e0d\u4e00\u6837"},"content":{"rendered":"
\n

RNA \u6d4b\u5e8f\u5b8c\u6210\u6bd4\u5bf9\u4e4b\u540e\uff0c\u5f88\u591a\u4eba\u9996\u5148\u67e5\u770b\u603b\u4f53\u6bd4\u5bf9\u7387\u3002\u8fd9\u4e2a\u6570\u5b57\u6709\u52a9\u4e8e\u53d1\u73b0\u4e25\u91cd\u7684\u53c2\u8003\u4e0d\u5339\u914d\u6216\u6570\u636e\u95ee\u9898\uff0c\u4f46\u5b83\u4e0d\u80fd\u544a\u8bc9\u6211\u4eec\u6bcf\u6761\u8bfb\u6bb5\u662f\u5426\u6309\u7167\u9884\u671f\u7684\u5916\u663e\u5b50\u7ed3\u6784\u5b8c\u6210\u6bd4\u5bf9\u3002\u8bfb\u6bb5\u7684\u4e00\u90e8\u5206\u53ef\u4ee5\u88ab\u8f6f\u526a\u5207\uff0c\u5269\u4e0b\u7684\u90e8\u5206\u4ecd\u7136\u6210\u529f\u5339\u914d\uff0c\u56e0\u6b64\u201c\u6bd4\u5bf9\u6210\u529f\u201d\u548c\u201c\u526a\u63a5\u8fde\u63a5\u88ab\u6b63\u786e\u8868\u793a\u201d\u662f\u4e24\u4e2a\u9700\u8981\u5206\u522b\u68c0\u67e5\u7684\u95ee\u9898\u3002<\/p>\n

\u672c\u6587\u5b9e\u9645\u5b89\u88c5 HISAT2 2.2.3\uff0c\u8bbe\u8ba1\u4e00\u4e2a\u53ea\u6709\u4e24\u4e2a\u5916\u663e\u5b50\u7684\u4eba\u5de5\u4f4d\u70b9\uff0c\u7528\u516d\u6761\u6ca1\u6709\u6d4b\u5e8f\u9519\u8bef\u7684\u8bfb\u6bb5\u505a\u56db\u7ec4\u5bf9\u7167\u3002\u672a\u63d0\u4f9b\u6ce8\u91ca\u4e0e\u63d0\u4f9b\u5df2\u77e5\u526a\u63a5\u4f4d\u70b9\u65f6\uff0c\u603b\u4f53\u6bd4\u5bf9\u7387\u90fd\u662f\u767e\u5206\u4e4b\u767e\uff0c\u4f46\u5176\u4e2d\u4e24\u6761\u8bfb\u6bb5\u7684\u6bd4\u5bf9\u7ed3\u6784\u53d1\u751f\u4e86\u660e\u663e\u53d8\u5316\u3002\u8fd9\u4e2a\u5b9e\u9a8c\u9002\u5408\u7528\u4e8e\u5b66\u4e60\u7ed3\u679c\u9605\u8bfb\uff0c\u4e0d\u7528\u4e8e\u4f30\u8ba1\u771f\u5b9e\u6837\u672c\u4e2d\u7684\u68c0\u51fa\u7387\u3002<\/p>\n

\"\u6bd4\u5bf9\u7387\u76f8\u540c\uff0c\u526a\u63a5\u7ed3\u6784\u5374\u4e0d\u540c\u3002\u516d\u6761\u8bbe\u8ba1\u8bfb\u6bb5\uff0c\u9010\u6761\u68c0\u67e5
\u516d\u6761\u8bbe\u8ba1\u8bfb\u6bb5\uff0c\u9010\u6761\u68c0\u67e5 CIGAR \u4e0e\u8fb9\u754c<\/figcaption><\/figure>\n

\u4e00\u3001\u5148\u660e\u786e HISAT2 \u5728\u56de\u7b54\u4ec0\u4e48\u95ee\u9898<\/h2>\n

HISAT2 \u5c06\u8bfb\u6bb5\u5b9a\u4f4d\u5230\u53c2\u8003\u5e8f\u5217\uff0c\u53ef\u4ee5\u5904\u7406\u8de8\u8d8a\u526a\u63a5\u4f4d\u7f6e\u7684\u6bd4\u5bf9\uff0c\u5e76\u8f93\u51fa\u540e\u7eed\u5de5\u5177\u80fd\u591f\u8bfb\u53d6\u7684 SAM\u3002\u5bf9\u4e8e\u666e\u901a\u77ed\u8bfb\u957f\u8f6c\u5f55\u7ec4\uff0c\u53c2\u8003\u901a\u5e38\u662f\u57fa\u56e0\u7ec4\uff0c\u6210\u719f\u8f6c\u5f55\u672c\u4e2d\u7684\u76f8\u90bb\u78b1\u57fa\u5728\u57fa\u56e0\u7ec4\u4e0a\u53ef\u80fd\u9694\u7740\u5f88\u957f\u7684\u5185\u542b\u5b50\u3002\u8fd9\u4e0e\u76f4\u63a5\u5c06\u8bfb\u6bb5\u5339\u914d\u5230\u8f6c\u5f55\u672c\u5e8f\u5217\u7684\u4efb\u52a1\u4e0d\u540c\u3002\u4f5c\u8005\u624b\u518c<\/a><\/p>\n

\u56e0\u6b64\uff0c\u8bc4\u4ef7\u4e00\u6b21\u6bd4\u5bf9\u81f3\u5c11\u9700\u8981\u540c\u65f6\u770b\u5b9a\u4f4d\u4f4d\u7f6e\u3001\u6bd4\u5bf9\u7ed3\u6784\u548c\u672a\u88ab\u89e3\u91ca\u7684\u78b1\u57fa\u3002\u53ea\u770b\u5b9a\u4f4d\u662f\u5426\u5b58\u5728\uff0c\u4f1a\u628a\u5b8c\u6574\u8de8\u8d8a\u8fde\u63a5\u7684\u8bfb\u6bb5\u548c\u4ec5\u4fdd\u7559\u4e00\u6bb5\u7684\u8bfb\u6bb5\u653e\u5728\u540c\u4e00\u4e2a\u201c\u6210\u529f\u201d\u7c7b\u522b\u4e2d\u3002\u82e5\u63a5\u4e0b\u6765\u8981\u7edf\u8ba1\u526a\u63a5\u4e8b\u4ef6\uff0c\u8fd9\u79cd\u5dee\u5f02\u4f1a\u76f4\u63a5\u5f71\u54cd\u652f\u6301\u8fde\u63a5\u7684\u8bc1\u636e\u91cf\u3002<\/p>\n

\u8fd9\u4e2a\u5de5\u5177\u7684\u4f18\u52bf\u662f\u80fd\u591f\u5c06\u57fa\u56e0\u7ec4\u5b9a\u4f4d\u4e0e\u526a\u63a5\u4fe1\u606f\u653e\u5728\u540c\u4e00\u7ed3\u679c\u4e2d\uff0c\u4fbf\u4e8e\u7ee7\u7eed\u68c0\u67e5\u8986\u76d6\u548c\u8fde\u63a5\u3002\u5c40\u9650\u662f\u7ed3\u679c\u4f9d\u8d56\u53c2\u8003\u3001\u5019\u9009\u526a\u63a5\u4f4d\u7f6e\u3001\u8bfb\u6bb5\u672c\u8eab\u7684\u4fe1\u606f\u91cf\u4e0e\u6240\u7528\u53c2\u6570\u3002\u63d0\u4f9b\u4e00\u4efd\u6ce8\u91ca\u6709\u65f6\u80fd\u5e2e\u52a9\u89e3\u91ca\u77ed\u951a\u5b9a\u8bfb\u6bb5\uff0c\u4f46\u6ce8\u91ca\u672c\u8eab\u4ecd\u9700\u8981\u6b63\u786e\u5339\u914d\u5f53\u524d\u53c2\u8003\u3002<\/p>\n

\u4e8c\u3001\u628a\u5b9e\u9a8c\u8bbe\u8ba1\u5230\u80fd\u591f\u9010\u6761\u89e3\u91ca<\/h2>\n

\u672c\u6b21\u4eba\u5de5\u53c2\u8003\u957f\u4e09\u5343\u78b1\u57fa\uff0c\u53ea\u6709\u4e00\u4e2a\u540d\u4e3a chrToy \u7684\u5e8f\u5217\u3002\u7b2c\u4e00\u6bb5\u5916\u663e\u5b50\u4f4d\u4e8e\u4e94\u767e\u96f6\u4e00\u81f3\u4e00\u5343\uff0c\u7b2c\u4e8c\u6bb5\u4f4d\u4e8e\u4e24\u5343\u96f6\u4e00\u81f3\u4e24\u5343\u4e94\u767e\uff0c\u4e2d\u95f4\u4e3a\u4e00\u5343\u78b1\u57fa\u5185\u542b\u5b50\u3002\u5916\u663e\u5b50\u53ca\u80cc\u666f\u6309\u56fa\u5b9a\u968f\u673a\u79cd\u5b50\u751f\u6210\uff0c\u5185\u542b\u5b50\u4e24\u7aef\u8bbe\u7f6e\u4e3a\u6b63\u94fe\u5e38\u89c1\u7684 GT \u548c AG\u3002<\/p>\n

\u516d\u6761\u8f93\u5165\u5747\u4e3a\u4e00\u767e\u4e94\u5341\u78b1\u57fa\uff0c\u8d28\u91cf\u5b57\u7b26\u4e00\u81f4\u3002\u9664\u4e86\u666e\u901a\u5916\u663e\u5b50\u8bfb\u6bb5\u548c\u8de8\u8d8a\u5916\u663e\u5b50\u4e0e\u5185\u542b\u5b50\u8fb9\u754c\u7684\u8fde\u7eed\u57fa\u56e0\u7ec4\u8bfb\u6bb5\uff0c\u8fd8\u6709\u56db\u6761\u8de8\u8d8a\u5916\u663e\u5b50\u8fde\u63a5\u7684\u8bfb\u6bb5\u3002\u56db\u6761\u8fde\u63a5\u8bfb\u6bb5\u5728\u5de6\u5916\u663e\u5b50\u4e0a\u5206\u522b\u5177\u6709\u4e03\u5341\u4e94\u3001\u5341\u4e8c\u3001\u516b\u3001\u56db\u4e2a\u78b1\u57fa\uff0c\u5176\u4f59\u90e8\u5206\u6765\u81ea\u53f3\u5916\u663e\u5b50\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n\n\n
\u8bfb\u6bb5\u7c7b\u578b<\/th>\n\u5de6\u4fa7 bp<\/th>\n\u53f3\u4fa7\u7ec4\u6210<\/th>\n\u7528\u9014<\/th>\n<\/tr>\n<\/thead>\n
\u5916\u663e\u5b50<\/td>\n150<\/td>\n\u4e0d\u8de8\u8fde\u63a5<\/td>\n\u5b9a\u4f4d\u5bf9\u7167<\/td>\n<\/tr>\n
\u63a5\u5934 75<\/td>\n75<\/td>\n\u5916\u663e\u5b50 75 bp<\/td>\n\u53cc\u4fa7\u8bc1\u636e<\/td>\n<\/tr>\n
\u63a5\u5934 12<\/td>\n12<\/td>\n\u5916\u663e\u5b50 138 bp<\/td>\n\u8f83\u77ed\u951a\u5b9a<\/td>\n<\/tr>\n
\u63a5\u5934 8<\/td>\n8<\/td>\n\u5916\u663e\u5b50 142 bp<\/td>\n\u66f4\u77ed\u951a\u5b9a<\/td>\n<\/tr>\n
\u63a5\u5934 4<\/td>\n4<\/td>\n\u5916\u663e\u5b50 146 bp<\/td>\n\u6781\u77ed\u951a\u5b9a<\/td>\n<\/tr>\n
\u8fde\u7eed\u57fa\u56e0\u7ec4<\/td>\n75<\/td>\n\u5185\u542b\u5b50 75 bp<\/td>\n\u8fde\u7eed\u5339\u914d<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u8fd9\u4e9b\u8bfb\u6bb5\u4e0d\u662f\u5b9e\u9645\u6d4b\u5e8f\u6837\u672c\uff0c\u6ca1\u6709\u5f15\u5165\u6d4b\u5e8f\u9519\u8bef\uff0c\u4e5f\u6ca1\u6709\u6a21\u62df\u590d\u6742\u91cd\u590d\u533a\u57df\u3002\u8fd9\u6837\u505a\u7684\u76ee\u7684\u662f\u51cf\u5c11\u5176\u4ed6\u56e0\u7d20\uff0c\u8ba9\u8bfb\u8005\u80fd\u628a\u53d8\u5316\u8ffd\u6eaf\u5230\u526a\u63a5\u5148\u9a8c\u548c\u8f6f\u526a\u5207\u3002\u5b9e\u9a8c\u8fc7\u4e8e\u7b80\u5355\uff0c\u4e0d\u80fd\u636e\u6b64\u5ba3\u79f0\u67d0\u7ec4\u53c2\u6570\u5728\u771f\u5b9e\u8f6c\u5f55\u7ec4\u91cc\u5177\u6709\u540c\u6837\u8868\u73b0\u3002<\/p>\n

\u8bfb\u8005\u8fd8\u5e94\u6ce8\u610f\uff0c\u77ed\u951a\u5b9a\u672c\u8eab\u4e0d\u7b49\u4e8e\u4f4e\u8d28\u91cf\u3002\u8fd9\u91cc\u6240\u6709\u78b1\u57fa\u8d28\u91cf\u90fd\u76f8\u540c\uff0c\u533a\u522b\u6765\u81ea\u80fd\u591f\u652f\u6491\u8fde\u63a5\u4e00\u4fa7\u7684\u5e8f\u5217\u957f\u5ea6\u3002\u771f\u5b9e\u6570\u636e\u4e2d\uff0c\u8d28\u91cf\u5dee\u3001\u540c\u6e90\u533a\u57df\u3001\u91cd\u590d\u7ed3\u6784\u4e0e\u77ed\u951a\u5b9a\u53ef\u80fd\u540c\u65f6\u5b58\u5728\uff0c\u9700\u8981\u5206\u5f00\u5224\u65ad\u3002<\/p>\n

\u4e09\u3001\u5df2\u77e5\u526a\u63a5\u4f4d\u70b9\u600e\u6837\u51c6\u5907\uff0c\u5750\u6807\u600e\u6837\u6838\u5bf9<\/h2>\n

\u6211\u4eec\u5148\u5199\u51fa\u4e24\u884c GTF \u5916\u663e\u5b50\u8bb0\u5f55\uff0c\u518d\u5b9e\u9645\u8c03\u7528\u5b89\u88c5\u5305\u4e2d\u7684\u63d0\u53d6\u811a\u672c\u3002\u8f93\u51fa\u4e3a chrToy\u3001999\u30012000\u3001\u6b63\u94fe\u6807\u8bb0\u3002\u8fd9\u4e24\u4e2a\u6570\u5b57\u4e0d\u662f\u5c06\u5185\u542b\u5b50\u7684\u9996\u5c3e\u4f4d\u7f6e\u539f\u6837\u590d\u5236\u8fc7\u53bb\u3002\u6700\u7a33\u59a5\u7684\u65b9\u6cd5\u662f\u8ba9\u914d\u5957\u811a\u672c\u4ece\u540c\u7248\u672c\u6ce8\u91ca\u63d0\u53d6\uff0c\u518d\u7528\u4e00\u4e2a\u53ef\u624b\u5de5\u68c0\u67e5\u7684\u4f4d\u70b9\u9a8c\u8bc1\u3002<\/p>\n

hisat2_extract_splice_sites.py genes.gtf > sites.tsv\r\nhisat2-build -p 2 genome.fna idx\r\n\r\nhisat2 -p 2 --no-temp-splicesite \\\r\n  -x idx -U reads.fq \\\r\n  --known-splicesite-infile sites.tsv \\\r\n  -S known.sam\r\n<\/code><\/pre>\n
\u5728\u672c\u4f8b\u4e2d\uff0cGTF \u4f7f\u7528\u7684\u4e00\u8d77\u59cb\u95ed\u533a\u95f4\u5916\u663e\u5b50\u5750\u6807\u662f 501\u20131000 \u4e0e 2001\u20132500\u3002\u63d0\u53d6\u6587\u4ef6\u8bb0\u5f55\u7684\u662f\u5bf9\u5e94\u8fb9\u754c\u7684\u96f6\u8d77\u59cb\u5750\u6807\uff0c\u5f97\u5230 999 \u4e0e 2000\u3002\u5b83\u4eec\u4e0e SAM \u4e2d\u7684\u4e00\u8d77\u59cb\u5b9a\u4f4d\u5b57\u6bb5\u3001\u4ee5\u53ca\u5185\u542b\u5b50\u7684\u533a\u95f4\u8868\u793a\u5404\u6709\u7528\u9014\uff0c\u4e0d\u5e94\u6df7\u7740\u52a0\u51cf\u4e00\u3002<\/p>\n
\u5b9e\u9645\u9879\u76ee\u91cc\uff0c\u6700\u5e38\u89c1\u7684\u51c6\u5907\u9519\u8bef\u5e76\u4e0d\u4e00\u5b9a\u662f\u547d\u4ee4\u62fc\u9519\uff0c\u800c\u662f\u67d3\u8272\u4f53\u540d\u79f0\u6216\u53c2\u8003\u7248\u672c\u4e0d\u4e00\u81f4\u3002\u540c\u4e00\u4e2a\u4f4d\u7f6e\u7f16\u53f7\u653e\u5230\u53e6\u4e00\u5957\u7ec4\u88c5\u4e0a\u672a\u5fc5\u8868\u793a\u540c\u4e00\u5e8f\u5217\uff0c\u5e26\u524d\u7f00\u4e0e\u4e0d\u5e26\u524d\u7f00\u7684\u540d\u79f0\u4e5f\u53ef\u80fd\u65e0\u6cd5\u5bf9\u5e94\u3002\u68c0\u67e5\u65f6\u53ef\u5148\u6bd4\u8f83\u540d\u79f0\u96c6\u5408\uff0c\u518d\u62bd\u67e5\u51e0\u4e2a\u5916\u663e\u5b50\u7684\u53c2\u8003\u5e8f\u5217\u548c\u8fde\u63a5\u4f4d\u7f6e\u3002<\/p>\n
\u672c\u6b21\u6240\u6709\u7ec4\u90fd\u989d\u5916\u5173\u95ed\u4e86\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u4e34\u65f6\u526a\u63a5\u4f4d\u70b9\u7684\u5171\u4eab\uff0c\u76ee\u7684\u662f\u9694\u79bb\u201c\u7ed9\u5b9a\u6ce8\u91ca\u201d\u7684\u4f5c\u7528\uff0c\u51cf\u5c11\u8bfb\u6bb5\u5904\u7406\u987a\u5e8f\u5bf9\u8fd9\u4e2a\u5c0f\u5b9e\u9a8c\u7684\u5f71\u54cd\u3002\u8fd9\u662f\u5b9e\u9a8c\u63a7\u5236\u6761\u4ef6\uff0c\u4e0d\u662f\u5efa\u8bae\u6240\u6709\u6b63\u5f0f\u9879\u76ee\u90fd\u7167\u642c\u8be5\u9009\u9879\u3002\u7406\u89e3\u4e00\u4e2a\u5bf9\u7167\u9700\u8981\u77e5\u9053\u54ea\u4e9b\u53d8\u91cf\u88ab\u56fa\u5b9a\uff0c\u4e0d\u80fd\u628a\u63a7\u5236\u6761\u4ef6\u81ea\u52a8\u5f53\u4f5c\u6700\u4f73\u5b9e\u8df5\u3002<\/p>\n
\u56db\u3001\u56db\u7ec4\u5b9e\u9645\u7ed3\u679c\uff0c\u4e0d\u80fd\u53ea\u6bd4\u8f83\u6210\u529f\u6bd4\u4f8b<\/h2>\n
\u56db\u7ec4\u4f9d\u6b21\u4e3a\u4e0d\u63d0\u4f9b\u5df2\u77e5\u526a\u63a5\u4f4d\u70b9\u3001\u63d0\u4f9b\u5df2\u77e5\u4f4d\u70b9\u3001\u63d0\u4f9b\u4f4d\u70b9\u5e76\u7981\u6b62\u8f6f\u526a\u5207\u3001\u5173\u95ed\u526a\u63a5\u6bd4\u5bf9\u3002\u524d\u4e09\u7ec4\u5168\u90e8\u516d\u6761\u6210\u529f\u5b9a\u4f4d\uff0c\u6700\u540e\u4e00\u7ec4\u4e3a\u4e94\u6761\u6210\u529f\u5b9a\u4f4d\u3002\u82e5\u53ea\u8bfb\u603b\u4f53\u6bd4\u4f8b\uff0c\u524d\u9762\u4e09\u7ec4\u770b\u8d77\u6765\u5b8c\u5168\u4e00\u6837\u3002<\/p>\n
\n\n\n\n\n\n\n\n\n
\u5de6\u53f3\u951a\u5b9a<\/th>\n\u4e0d\u63d0\u4f9b\u4f4d\u70b9<\/th>\n\u5df2\u77e5\u4f4d\u70b9<\/th>\n\u5173\u95ed\u526a\u63a5<\/th>\n<\/tr>\n<\/thead>\n
75 \/ 75<\/td>\n75M1000N75M<\/td>\n75M1000N75M<\/td>\n\u672a\u6bd4\u5bf9<\/td>\n<\/tr>\n
12 \/ 138<\/td>\n12M1000N138M<\/td>\n12M1000N138M<\/td>\n11S139M<\/td>\n<\/tr>\n
8 \/ 142<\/td>\n7S143M<\/td>\n8M1000N142M<\/td>\n7S143M<\/td>\n<\/tr>\n
4 \/ 146<\/td>\n3S147M<\/td>\n4M1000N146M<\/td>\n3S147M<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u4e0d\u63d0\u4f9b\u4f4d\u70b9\u65f6\uff0c\u56db\u6761\u771f\u6b63\u8de8\u8d8a\u8fde\u63a5\u7684\u8bbe\u8ba1\u8bfb\u6bb5\u4e2d\u53ea\u6709\u4e24\u6761\u88ab\u8868\u793a\u6210\u526a\u63a5\u6bd4\u5bf9\u3002\u63d0\u4f9b\u4f4d\u70b9\u540e\uff0c\u56db\u6761\u90fd\u51fa\u73b0\u4e86\u4e0e\u8bbe\u8ba1\u7ed3\u6784\u4e00\u81f4\u7684\u8df3\u8dc3\u3002\u7981\u6b62\u8f6f\u526a\u5207\u7684\u5df2\u77e5\u4f4d\u70b9\u7ec4\u5728\u672c\u6b21\u8f93\u5165\u4e0a\u4e0e\u666e\u901a\u5df2\u77e5\u4f4d\u70b9\u7ec4\u4e00\u81f4\uff0c\u6ca1\u6709\u589e\u52a0\u65b0\u7684\u6210\u529f\u8bb0\u5f55\u3002<\/p>\n
\u8fd9\u8bf4\u660e\u603b\u4f53\u6bd4\u5bf9\u7387\u6ca1\u6709\u8986\u76d6\u6211\u4eec\u771f\u6b63\u5173\u5fc3\u7684\u5dee\u522b\u3002\u5bf9\u4e8e\u8fde\u63a5\u5206\u6790\uff0c\u66f4\u76f4\u63a5\u7684\u6838\u9a8c\u662f\u9010\u6761\u68c0\u67e5\u54ea\u4e9b\u8bfb\u6bb5\u542b\u6709\u8de8\u5185\u542b\u5b50\u7684\u7ed3\u6784\uff0c\u8df3\u8dc3\u957f\u5ea6\u662f\u5426\u6b63\u786e\uff0c\u5de6\u53f3\u652f\u6301\u5206\u522b\u591a\u957f\u3002\u6210\u529f\u5b9a\u4f4d\u53ea\u5b8c\u6210\u4e86\u5176\u4e2d\u4e00\u90e8\u5206\u68c0\u67e5\u3002<\/p>\n
\u5173\u95ed\u526a\u63a5\u6bd4\u5bf9\u540e\uff0c\u4e03\u5341\u4e94\u6bd4\u4e03\u5341\u4e94\u7684\u8fde\u63a5\u8bfb\u6bb5\u65e0\u6cd5\u4ee5\u672c\u6b21\u6761\u4ef6\u5b8c\u6210\u8fde\u7eed\u5339\u914d\uff0c\u4f46\u4e09\u6761\u77ed\u951a\u5b9a\u8bfb\u6bb5\u4ecd\u7136\u88ab\u4fdd\u7559\u4e3a\u8f6f\u526a\u5207\u7ed3\u679c\u3002\u4e0d\u80fd\u56e0\u4e3a\u5b83\u4eec\u4ecd\u5728 SAM \u4e2d\u4e14\u663e\u793a\u6210\u529f\uff0c\u5c31\u8ba4\u4e3a\u5173\u95ed\u526a\u63a5\u4e0d\u4f1a\u5f71\u54cd\u8be5\u533a\u57df\u7684\u5206\u6790\u3002<\/p>\n
\u4e94\u3001\u628a CIGAR \u5f53\u4f5c\u89e3\u91ca\u7ed3\u679c\u7684\u4e3b\u7ebf<\/h2>\n
\u5728\u672c\u6b21\u7ed3\u679c\u4e2d\uff0cM \u63cf\u8ff0\u53c2\u52a0\u6bd4\u5bf9\u7684\u8bfb\u6bb5\u78b1\u57fa\uff0cN \u63cf\u8ff0\u53c2\u8003\u4e0a\u7684\u8df3\u8dc3\uff0cS \u63cf\u8ff0\u4fdd\u7559\u5728\u8bfb\u6bb5\u5e8f\u5217\u4e2d\u4f46\u672a\u53c2\u52a0\u5f53\u524d\u6bd4\u5bf9\u7684\u8f6f\u526a\u5207\u90e8\u5206\u3002M \u672c\u8eab\u4e0d\u4fdd\u8bc1\u6240\u6709\u78b1\u57fa\u90fd\u5b8c\u5168\u4e00\u81f4\uff0c\u8fd8\u5e94\u7ed3\u5408\u5dee\u5f02\u6807\u7b7e\u68c0\u67e5\u3002SAM \u683c\u5f0f\u89c4\u8303<\/a><\/p>\n
\u4ee5 8M1000N142M \u4e3a\u4f8b\uff0c\u5de6\u53f3\u53c2\u52a0\u6bd4\u5bf9\u7684\u8bfb\u6bb5\u957f\u5ea6\u52a0\u8d77\u6765\u662f\u4e00\u767e\u4e94\u5341\uff0c\u4e2d\u95f4\u8df3\u8fc7\u4e00\u5343\u4e2a\u53c2\u8003\u78b1\u57fa\u3002\u5185\u542b\u5b50\u957f\u5ea6\u6d88\u8017\u7684\u662f\u53c2\u8003\u5750\u6807\uff0c\u4e0d\u989d\u5916\u6d88\u8017\u8bfb\u6bb5\u957f\u5ea6\u3002\u82e5\u628a\u8fd9\u4e00\u5343\u4e5f\u7b97\u5230\u8bfb\u6bb5\u957f\u5ea6\u91cc\uff0c\u5c31\u4f1a\u5f97\u5230\u660e\u663e\u9519\u8bef\u7684\u8986\u76d6\u6216\u8fde\u63a5\u957f\u5ea6\u3002<\/p>\n
\u518d\u770b 7S143M\u3002\u5b83\u5e76\u4e0d\u4ee3\u8868\u7a0b\u5e8f\u5fd8\u8bb0\u8f93\u5165\u539f\u672c\u6709\u516b\u4e2a\u78b1\u57fa\u6765\u81ea\u5de6\u5916\u663e\u5b50\u3002\u5f53\u524d\u8fde\u7eed\u5339\u914d\u8fd8\u53ef\u4ee5\u5229\u7528\u8fb9\u754c\u9644\u8fd1\u4e00\u4e2a\u6070\u597d\u76f8\u540c\u7684\u78b1\u57fa\uff0c\u6240\u4ee5\u6700\u7ec8\u8f6f\u526a\u5207\u957f\u5ea6\u4e0e\u8bbe\u8ba1\u4e2d\u7684\u5de6\u4fa7\u951a\u5b9a\u957f\u5ea6\u76f8\u5dee\u4e00\u3002\u5b9e\u9645\u8d77\u59cb\u4f4d\u7f6e\u4e3a\u4e24\u5343\uff0c\u5305\u542b\u5185\u542b\u5b50\u672b\u7aef\u7684\u90a3\u4e2a\u78b1\u57fa\u3002\u8bfb\u8005\u9700\u8981\u540c\u65f6\u6838\u5bf9\u5e8f\u5217\u548c\u5750\u6807\uff0c\u4e0d\u80fd\u4ec5\u51ed\u8f6f\u526a\u5207\u957f\u5ea6\u53cd\u63a8\u771f\u5b9e\u526a\u63a5\u7ed3\u6784\u3002<\/p>\n
\u56db\u78b1\u57fa\u951a\u5b9a\u8bfb\u6bb5\u4e5f\u6709\u540c\u7c7b\u73b0\u8c61\uff0c\u5b9e\u9645\u4e3a 3S147M\u3002\u8fd9\u4e2a\u5c0f\u4f8b\u5b50\u63d0\u9192\u6211\u4eec\uff0c\u6bd4\u5bf9\u7b97\u6cd5\u4f1a\u5bfb\u627e\u7b26\u5408\u8bc4\u5206\u7684\u89e3\u91ca\uff0c\u800c\u4e0d\u662f\u8bfb\u53d6\u5b9e\u9a8c\u8005\u5fc3\u4e2d\u9884\u8bbe\u7684\u6765\u6e90\u6807\u7b7e\u3002\u5b58\u5728\u4e00\u4e2a\u53ef\u63a5\u53d7\u7684\u8fde\u7eed\u89e3\u91ca\u65f6\uff0c\u6b63\u786e\u7684\u751f\u7269\u5b66\u6765\u6e90\u4e0d\u4f1a\u81ea\u52a8\u5199\u8fdb\u7ed3\u679c\u3002<\/p>\n
\u56e0\u6b64\uff0c\u82e5\u770b\u5230\u5f88\u591a\u672b\u7aef\u8f6f\u526a\u5207\uff0c\u5e94\u5148\u5224\u65ad\u5b83\u4eec\u662f\u5426\u96c6\u4e2d\u5728\u8fde\u63a5\u9644\u8fd1\u3001\u662f\u5426\u53d7\u5230\u6ce8\u91ca\u5f71\u54cd\u3001\u662f\u5426\u540c\u65f6\u51fa\u73b0\u5728\u91cd\u590d\u533a\u6216\u4f4e\u8d28\u91cf\u533a\u3002\u4e0d\u8981\u770b\u5230\u4e00\u4e2a\u8f6f\u526a\u5207\u5c31\u76f4\u63a5\u547d\u540d\u4e3a\u65b0\u526a\u63a5\u3001\u878d\u5408\u6216\u7ed3\u6784\u53d8\u5f02\uff0c\u4e5f\u4e0d\u8981\u5728\u6ca1\u6709\u770b\u5e8f\u5217\u7684\u60c5\u51b5\u4e0b\u5168\u90e8\u4e22\u6389\u3002<\/p>\n
\u516d\u3001MAPQ \u5f88\u9ad8\uff0c\u4e3a\u4ec0\u4e48\u4ecd\u7136\u9700\u8981\u770b\u7ed3\u6784<\/h2>\n
\u672c\u6b21\u6210\u529f\u5b9a\u4f4d\u7684\u8bfb\u6bb5 MAPQ \u90fd\u4e3a\u516d\u5341\uff0c\u5305\u62ec\u90a3\u4e9b\u77ed\u951a\u5b9a\u8bfb\u6bb5\u7684\u8f6f\u526a\u5207\u7ed3\u679c\u3002\u8fd9\u4e2a\u73b0\u8c61\u5f88\u6709\u6559\u5b66\u4ef7\u503c\uff0c\u56e0\u4e3a\u5b83\u76f4\u63a5\u8bf4\u660e\u4e00\u4e2a\u8f83\u9ad8\u7684\u5b9a\u4f4d\u8d28\u91cf\u6570\u5b57\u5e76\u4e0d\u7b49\u4ef7\u4e8e\u201c\u6574\u6761\u8bfb\u6bb5\u5df2\u7ecf\u6309\u9884\u671f\u7684\u8f6c\u5f55\u7ed3\u6784\u89e3\u91ca\u201d\u3002<\/p>\n
\u5b9a\u4f4d\u8d28\u91cf\u3001\u6bd4\u5bf9\u8bc4\u5206\u3001\u78b1\u57fa\u5dee\u5f02\u548c\u526a\u63a5\u7ed3\u6784\u63cf\u8ff0\u7684\u662f\u4e0d\u540c\u65b9\u9762\u3002\u5c06\u5b83\u4eec\u538b\u6210\u5355\u4e00\u901a\u8fc7\u6761\u4ef6\u4f1a\u4e22\u5931\u4fe1\u606f\u3002\u5bf9\u4e8e\u4e00\u4e2a\u91cd\u70b9\u8fde\u63a5\uff0c\u53ef\u4ee5\u540c\u65f6\u8bb0\u5f55\u5b9a\u4f4d\u662f\u5426\u552f\u4e00\u3001\u5de6\u53f3\u951a\u5b9a\u957f\u5ea6\u3001\u662f\u5426\u5b58\u5728\u8f6f\u526a\u5207\u3001\u8df3\u8dc3\u662f\u5426\u5bf9\u5e94\u6ce8\u91ca\uff0c\u4ee5\u53ca\u652f\u6301\u6765\u81ea\u591a\u5c11\u72ec\u7acb\u7247\u6bb5\u3002<\/p>\n
\u8fd9\u91cc\u4e5f\u4e0d\u5e94\u53cd\u8fc7\u6765\u58f0\u79f0\u9ad8 MAPQ \u6ca1\u7528\u3002\u5b83\u4ecd\u7136\u662f\u7ed3\u679c\u5ba1\u9605\u7684\u4e00\u90e8\u5206\uff0c\u53ea\u662f\u9700\u8981\u653e\u5728\u6240\u56de\u7b54\u7684\u95ee\u9898\u4e2d\u3002\u82e5\u76ee\u6807\u662f\u68c0\u67e5\u5b9a\u4f4d\u6b67\u4e49\uff0c\u5b83\u4e0e\u76ee\u6807\u76f8\u5173\u3002\u82e5\u76ee\u6807\u662f\u8bc1\u5b9e\u67d0\u4e2a\u5916\u663e\u5b50\u8fde\u63a5\uff0c\u5219\u9700\u8981\u989d\u5916\u68c0\u67e5\u8fde\u63a5\u672c\u8eab\u7684\u8bc1\u636e\u3002<\/p>\n
\u5b9e\u9645\u7edf\u8ba1 SAM \u65f6\uff0c\u5e94\u6309\u6807\u8bb0\u8bc6\u522b\u672a\u6bd4\u5bf9\u548c\u6b21\u7ea7\u8bb0\u5f55\uff0c\u4e0d\u80fd\u4ec5\u7528\u6587\u4ef6\u884c\u6570\u4f5c\u4e3a\u8bfb\u6bb5\u6570\u91cf\u3002\u672c\u6b21\u6bcf\u4e2a\u8f93\u5165\u53ea\u6709\u4e00\u4e2a\u5bf9\u5e94\u8bb0\u5f55\uff0c\u590d\u6742\u6837\u672c\u53ef\u80fd\u4e3a\u540c\u4e00\u8bfb\u6bb5\u63d0\u4f9b\u591a\u4e2a\u8bb0\u5f55\u3002\u5206\u6bcd\u4e00\u65e6\u4ece\u72ec\u7acb\u8bfb\u6bb5\u53d8\u6210\u8bb0\u5f55\u884c\u6570\uff0c\u6bd4\u4f8b\u89e3\u91ca\u5c31\u4f1a\u6539\u53d8\u3002<\/p>\n
\u4e03\u3001\u57fa\u56e0\u7ec4\u8fde\u7eed\u5339\u914d\u4e5f\u4e0d\u80fd\u76f4\u63a5\u8bc1\u660e\u6c61\u67d3<\/h2>\n
\u672c\u6b21\u540d\u4e3a unspliced_DNA \u7684\u5bf9\u7167\u6765\u81ea\u5916\u663e\u5b50\u4e0e\u5185\u542b\u5b50\u7684\u8fde\u7eed\u57fa\u56e0\u7ec4\u5e8f\u5217\uff0c\u5728\u56db\u7ec4\u4e2d\u90fd\u662f 150M\u3002\u8fd9\u4e2a\u540d\u5b57\u63cf\u8ff0\u6211\u4eec\u600e\u6837\u751f\u6210\u8f93\u5165\uff0c\u5e76\u4e0d\u662f\u5de5\u5177\u6839\u636e\u5e8f\u5217\u81ea\u52a8\u7ed9\u51fa\u7684\u6837\u672c\u8bca\u65ad\u3002\u8f6f\u4ef6\u53ea\u5b8c\u6210\u4e86\u8fde\u7eed\u5b9a\u4f4d\uff0c\u6ca1\u6709\u8bc1\u660e\u771f\u5b9e\u6837\u672c\u5b58\u5728\u67d0\u4e00\u79cd\u6c61\u67d3\u3002<\/p>\n
\u5728\u771f\u5b9e RNA \u6570\u636e\u91cc\uff0c\u5185\u542b\u5b50\u76f8\u5173\u4fe1\u53f7\u53ef\u80fd\u4e0e\u5b9e\u9a8c\u65b9\u6848\u3001\u672a\u6210\u719f\u8f6c\u5f55\u672c\u3001\u5185\u542b\u5b50\u4fdd\u7559\u3001\u57fa\u56e0\u7ec4 DNA \u6b8b\u7559\u6216\u5176\u4ed6\u56e0\u7d20\u6709\u5173\u3002\u5e94\u7ed3\u5408\u6587\u5e93\u5236\u5907\u3001\u5168\u5c40\u5206\u5e03\u3001\u72ec\u7acb\u9a8c\u8bc1\u4e0e\u6ce8\u91ca\u80cc\u666f\u5206\u6790\uff0c\u4e0d\u80fd\u628a\u672c\u6b21\u4eba\u4e3a\u547d\u540d\u76f4\u63a5\u63a8\u5e7f\u6210\u5224\u5b9a\u89c4\u5219\u3002<\/p>\n
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