{"id":73131,"date":"2026-11-15T13:59:43","date_gmt":"2026-11-15T05:59:43","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=73131"},"modified":"2026-11-15T14:01:01","modified_gmt":"2026-11-15T06:01:01","slug":"isoseq-collapse-five-prime-truncation-end-threshold-model-practice","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/isoseq-collapse-five-prime-truncation-end-threshold-model-practice\/","title":{"rendered":"Iso-Seq collapse \u5b9e\u8dd1\uff0c\u6a21\u578b\u4ece\u4e94\u4e2a\u53d8\u4e24\u4e2a\u4ee5\u540e\uff0c\u8fd8\u5e94\u8be5\u68c0\u67e5\u4ec0\u4e48"},"content":{"rendered":"
\n

\u957f\u8bfb\u957f\u8f6c\u5f55\u7ec4\u5206\u6790\u5e38\u628a\u53bb\u5197\u4f59\u540e\u7684\u6a21\u578b\u6570\u91cf\u5f53\u4f5c\u4e00\u4e2a\u91cd\u8981\u7ed3\u679c\u3002\u6a21\u578b\u51cf\u5c11\uff0c\u53ef\u80fd\u610f\u5473\u7740\u91cd\u590d\u7ed3\u6784\u88ab\u5408\u5e76\uff0c\u4e5f\u53ef\u80fd\u610f\u5473\u7740\u4e0d\u540c\u8d77\u6b62\u8fb9\u754c\u6216\u4e0d\u5b8c\u6574\u7ed3\u6784\u88ab\u653e\u8fdb\u4e86\u540c\u4e00\u7ec4\u3002\u53ea\u770b\u6700\u7ec8\u6761\u6570\uff0c\u5f88\u96be\u5224\u65ad\u8fd9\u6b21\u53d8\u5316\u662f\u5426\u7b26\u5408\u7814\u7a76\u76ee\u6807\u3002<\/p>\n

\u672c\u7bc7\u5b9e\u9645\u8fd0\u884c Iso-Seq \u4e8c\u5341\u516d\u70b9\u4e8c\u70b9\u96f6\u7684\u7ed3\u6784\u5f52\u5e76\u6a21\u5757\u3002\u6211\u4eec\u6784\u9020\u5341\u4e00\u6761\u80fd\u591f\u9010\u9879\u6838\u5bf9\u7684\u8f6c\u5f55\u672c\u7ea7\u6bd4\u5bf9\u8bb0\u5f55\uff0c\u53ea\u8c03\u6574\u5f52\u5e76\u53c2\u6570\uff0c\u5f97\u5230\u4e24\u4e2a\u3001\u56db\u4e2a\u548c\u4e94\u4e2a\u6a21\u578b\u3002\u9664\u4e86\u6bd4\u8f83\u6570\u91cf\uff0c\u8fd8\u68c0\u67e5\u6bcf\u4e2a\u6a21\u578b\u7684\u5916\u663e\u5b50\u7ed3\u6784\u548c\u6210\u5458\u6765\u6e90\uff0c\u8bf4\u660e\u4e3a\u4ec0\u4e48\u652f\u6301\u603b\u6570\u4e0d\u80fd\u4ee3\u66ff\u5b8c\u6574\u7ed3\u6784\u7684\u652f\u6301\u8bc1\u636e\u3002<\/p>\n

\"\u6a21\u578b\u53d8\u5c11\uff0c\u8fd8\u8981\u6838\u5bf9\u4ee3\u8868\u7ed3\u6784\u3002\u5341\u4e00\u6761\u8bbe\u8ba1\u8bb0\u5f55\uff0c\u6bd4\u8f83\u5f52\u5e76\u7c92\u5ea6\u4e0e\u6210\u5458\u6765\u6e90\u30022
\u5341\u4e00\u6761\u8bbe\u8ba1\u8bb0\u5f55\uff0c\u6bd4\u8f83\u5f52\u5e76\u7c92\u5ea6\u4e0e\u6210\u5458\u6765\u6e90<\/figcaption><\/figure>\n

\u5148\u660e\u786e\u672c\u7bc7\u8fd0\u884c\u7684\u662f\u54ea\u4e00\u6b65<\/h2>\n

\u4ece\u539f\u59cb\u957f\u8bfb\u6bb5\u5230\u6700\u7ec8\u6a21\u578b\uff0c\u4e2d\u95f4\u53ef\u80fd\u7ecf\u5386\u5f15\u7269\u5904\u7406\u3001\u5168\u957f\u975e\u5d4c\u5408\u5e8f\u5217\u6574\u7406\u3001\u5e8f\u5217\u805a\u7c7b\u3001\u57fa\u56e0\u7ec4\u6bd4\u5bf9\u4ee5\u53ca\u7ed3\u6784\u5f52\u5e76\u3002\u524d\u9762\u5f97\u5230\u7684\u5e8f\u5217\u76f8\u4f3c\u6027\u4e0e\u540e\u9762\u5f97\u5230\u7684\u5916\u663e\u5b50\u7ed3\u6784\u76f8\u5bb9\u6027\uff0c\u662f\u4e0d\u540c\u5c42\u9762\u7684\u5224\u65ad\u3002<\/p>\n

\u672c\u7bc7\u53ea\u6d4b\u8bd5\u6700\u540e\u7684\u7ed3\u6784\u5f52\u5e76\u3002\u8f93\u5165\u4e0d\u662f\u5b9e\u9645\u6d4b\u5e8f\u6570\u636e\uff0c\u800c\u662f\u6309\u8bbe\u8ba1\u5199\u51fa\u7684 SAM \u8bb0\u5f55\uff0c\u518d\u901a\u8fc7 Samtools \u8f6c\u6210\u6392\u5e8f\u548c\u7d22\u5f15\u5b8c\u6210\u7684 BAM\u3002\u6211\u4eec\u6ca1\u6709\u8fd0\u884c\u539f\u59cb\u8bfb\u6bb5\u5904\u7406\u3001\u5e8f\u5217\u805a\u7c7b\u3001\u57fa\u56e0\u7ec4\u6bd4\u5bf9\u3001\u6761\u5f62\u7801\u6821\u6b63\u6216\u5206\u5b50\u53bb\u91cd\u3002<\/p>\n

\u8fd9\u6837\u505a\u7684\u597d\u5904\u662f\u53ef\u4ee5\u51c6\u786e\u63a7\u5236\u6bcf\u4e00\u6761\u8bb0\u5f55\u7684\u5916\u663e\u5b50\u8fb9\u754c\uff0c\u628a\u53c2\u6570\u5f71\u54cd\u4e0e\u4e0a\u6e38\u6bd4\u5bf9\u9519\u8bef\u5206\u5f00\u3002\u9650\u5236\u4e5f\u5f88\u660e\u786e\uff0c\u5b9e\u9a8c\u53ea\u80fd\u8bf4\u660e\u8fd9\u4e9b\u4eba\u5de5\u7ed3\u6784\u5728\u5f53\u524d\u7248\u672c\u4e2d\u7684\u5904\u7406\u7ed3\u679c\uff0c\u4e0d\u80fd\u8bc4\u4f30\u771f\u5b9e\u6837\u672c\u51c6\u786e\u7387\uff0c\u66f4\u4e0d\u80fd\u7ed9\u51fa\u5e73\u53f0\u4e4b\u95f4\u7684\u6027\u80fd\u6392\u540d\u3002<\/p>\n

\u867d\u7136\u7248\u672c\u4fe1\u606f\u5217\u51fa\u4e86\u7a0b\u5e8f\u94fe\u63a5\u7684\u591a\u4e2a\u7ec4\u4ef6\uff0c\u4e5f\u4e0d\u80fd\u636e\u6b64\u58f0\u79f0\u8fd9\u4e9b\u7ec4\u4ef6\u90fd\u5728\u5b9e\u9a8c\u4e2d\u5b9e\u9645\u6267\u884c\u8fc7\u3002\u5b89\u88c5\u73af\u5883\u5305\u542b\u67d0\u9879\u80fd\u529b\u4e0e\u5206\u6790\u786e\u5b9e\u8c03\u7528\u8be5\u80fd\u529b\uff0c\u9700\u8981\u7531\u547d\u4ee4\u548c\u65e5\u5fd7\u533a\u5206\u3002<\/p>\n

\u5341\u4e00\u6761\u8f93\u5165\u8bb0\u5f55\u5982\u4f55\u8bbe\u8ba1<\/h2>\n

\u53c2\u8003\u533a\u57df\u5305\u542b\u4e09\u4e2a\u5916\u663e\u5b50\uff0c\u4e00\u57fa\u5236\u95ed\u533a\u95f4\u5206\u522b\u4e3a\u4e00\u5343\u96f6\u4e00\u5230\u4e00\u5343\u56db\u767e\u3001\u4e8c\u5343\u4e94\u767e\u96f6\u4e00\u5230\u4e8c\u5343\u4e5d\u767e\u3001\u56db\u5343\u96f6\u4e00\u5230\u56db\u5343\u56db\u767e\u3002\u6211\u4eec\u628a\u8fd9\u4e2a\u7ed3\u6784\u79f0\u4e3a\u5b8c\u6574\u7ec4\uff0c\u751f\u6210\u4e09\u6761\u72ec\u7acb\u547d\u540d\u7684\u8f93\u5165\u8bb0\u5f55\u3002<\/p>\n

\u518d\u6784\u9020\u56db\u79cd\u53d8\u5316\uff0c\u6bcf\u79cd\u4e24\u6761\u8bb0\u5f55\u3002\u7b2c\u4e00\u79cd\u5220\u9664\u6700\u524d\u9762\u7684\u6574\u4e2a\u5916\u663e\u5b50\uff0c\u4fdd\u7559\u540e\u4e24\u4e2a\u3002\u7b2c\u4e8c\u79cd\u4fdd\u7559\u4e09\u4e2a\u5916\u663e\u5b50\uff0c\u4f46\u628a\u7b2c\u4e00\u4e2a\u5916\u663e\u5b50\u7684\u8d77\u70b9\u5411\u540e\u79fb\u52a8\u4e03\u5341\u78b1\u57fa\u3002\u7b2c\u4e09\u79cd\u628a\u6700\u540e\u5916\u663e\u5b50\u7684\u7ec8\u70b9\u5ef6\u957f\u4e03\u5341\u78b1\u57fa\u3002\u7b2c\u56db\u79cd\u628a\u7b2c\u4e00\u4e2a\u5916\u663e\u5b50\u7684\u4f9b\u4f53\u4f4d\u7f6e\u5ef6\u957f\u4e94\u5341\u78b1\u57fa\uff0c\u6539\u53d8\u5185\u90e8\u526a\u63a5\u8fb9\u754c\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n\n
\u8bbe\u8ba1\u7ec4<\/th>\n\u6761\u6570<\/th>\n\u4e0e\u5b8c\u6574\u7ec4\u7684\u533a\u522b<\/th>\n<\/tr>\n<\/thead>\n
\u5b8c\u6574<\/td>\n3<\/td>\n\u4e09\u5916\u663e\u5b50\u53c2\u8003\u7ed3\u6784<\/td>\n<\/tr>\n
\u7f3a\u9996\u6bb5<\/td>\n2<\/td>\n\u7f3a\u5931\u9996\u4e2a\u5916\u663e\u5b50<\/td>\n<\/tr>\n
\u9996\u7aef\u540e\u79fb<\/td>\n2<\/td>\n\u9996\u7aef\u5411\u540e\u79fb\u52a8 70 bp<\/td>\n<\/tr>\n
\u672b\u7aef\u5ef6\u957f<\/td>\n2<\/td>\n\u672b\u7aef\u5ef6\u957f 70 bp<\/td>\n<\/tr>\n
\u65b0\u4f9b\u4f53<\/td>\n2<\/td>\n\u5185\u90e8\u4f9b\u4f53\u6539\u53d8 50 bp<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u524d\u4e09\u7c7b\u53d8\u5316\u8ba9\u6211\u4eec\u533a\u5206\u7f3a\u5931\u6574\u4e2a\u5916\u663e\u5b50\u3001\u540c\u4e00\u5916\u663e\u5b50\u5185\u90e8\u7684\u7aef\u70b9\u5dee\u5f02\u548c\u672b\u7aef\u5dee\u5f02\u3002\u65b0\u4f9b\u4f53\u7ec4\u5219\u7528\u4e8e\u68c0\u67e5\u771f\u6b63\u6539\u53d8\u5185\u90e8\u526a\u63a5\u8fb9\u754c\u7684\u7ed3\u6784\u662f\u5426\u4ecd\u7136\u5355\u72ec\u4fdd\u7559\u3002<\/p>\n

\u6bcf\u6761\u8bb0\u5f55\u7684\u5e8f\u5217\u7531\u4eba\u5de5\u57fa\u56e0\u7ec4\u5bf9\u5e94\u533a\u95f4\u62fc\u63a5\uff0c\u5e76\u5199\u5165\u7cbe\u786e\u5339\u914d\u7684 CIGAR\u3002\u6240\u6709\u6765\u6e90\u540d\u79f0\u548c\u652f\u6301\u6807\u7b7e\u4e5f\u90fd\u662f\u6d4b\u8bd5\u7528\u6784\u9020\u503c\uff0c\u6bcf\u6761\u8f93\u5165\u5173\u8054\u4e00\u4e2a\u4eba\u5de5\u6765\u6e90\u540d\u3002\u5b83\u4eec\u4e0d\u662f\u5b9e\u9645\u6d4b\u5e8f\u4eea\u4ea7\u751f\u7684\u5206\u5b50\u8bb0\u5f55\uff0c\u4e5f\u6ca1\u6709\u627f\u62c5\u771f\u5b9e\u5b9e\u9a8c\u53bb\u91cd\u7684\u542b\u4e49\u3002<\/p>\n

\u7528\u56fa\u5b9a\u7248\u672c\u8fd0\u884c\u4e09\u7ec4\u6bd4\u8f83<\/h2>\n

\u672c\u6b21\u5bb9\u5668\u5185\u7a0b\u5e8f\u62a5\u544a\u4e8c\u5341\u516d\u70b9\u4e8c\u70b9\u96f6\uff0c\u4e09\u4e2a\u5f52\u5e76\u547d\u4ee4\u5747\u6b63\u5e38\u9000\u51fa\u3002\u9a71\u52a8\u4f7f\u7528\u56fa\u5b9a\u6458\u8981\u955c\u50cf\uff0c\u4fdd\u7559\u8bbe\u8ba1\u8f93\u5165\u3001\u6a21\u578b\u6587\u4ef6\u3001\u6210\u5458\u8868\u3001\u6765\u6e90\u8868\u548c\u65e5\u5fd7\u3002\u4e0b\u9762\u7684\u7248\u672c\u68c0\u67e5\u548c\u91cd\u8dd1\u5165\u53e3\u53ef\u4ee5\u76f4\u63a5\u590d\u73b0\u3002<\/p>\n

IMAGE=quay.io\/biocontainers\/isoseq@sha256:a2936a2c9249e4a5b471501af5fa09704d7356cc98042755b510087ee9a1638f\r\ndocker pull "$IMAGE"\r\ndocker run --rm "$IMAGE" isoseq --version\r\ndocker run --rm "$IMAGE" isoseq collapse --help\r\n\r\npython3 152-isoseq\/run.py results\/isoseq\r\n<\/code><\/pre>\n
\u9a71\u52a8\u5728 Linux \u4e3b\u673a\u6267\u884c\uff0c\u901a\u8fc7\u5bb9\u5668\u8c03\u7528\u8f6f\u4ef6\u3002\u4eba\u5de5 SAM \u7684\u8f6c\u6362\u3001\u6392\u5e8f\u548c\u7d22\u5f15\u540c\u6837\u5b9e\u9645\u5b8c\u6210\uff0c\u5e76\u6267\u884c\u4e86\u5feb\u901f\u683c\u5f0f\u68c0\u67e5\u3002\u683c\u5f0f\u68c0\u67e5\u53ea\u80fd\u5e2e\u52a9\u53d1\u73b0\u6587\u4ef6\u5c42\u9762\u7684\u95ee\u9898\uff0c\u4e0d\u80fd\u8bc1\u660e\u4eba\u5de5\u8f93\u5165\u5c31\u662f\u751f\u7269\u5b66\u4e0a\u53ef\u4fe1\u7684\u8f6c\u5f55\u672c\u3002<\/p>\n
\u4e09\u4e2a\u6838\u5fc3\u547d\u4ee4\u5982\u4e0b\uff0c\u5747\u4f7f\u7528\u540c\u4e00\u4efd\u5df2\u7ecf\u6392\u5e8f\u7684\u6bd4\u5bf9\u6587\u4ef6\u3002\u4e3a\u4e86\u8ba9\u7ed3\u679c\u5bb9\u6613\u8ffd\u8e2a\uff0c\u5206\u522b\u5199\u5165\u72ec\u7acb\u524d\u7f00\u3002<\/p>\n
isoseq collapse -j 2 --log-level INFO \\\r\n  mapped.bam default.gff\r\n\r\nisoseq collapse -j 2 --log-level INFO \\\r\n  --do-not-collapse-extra-5exons \\\r\n  mapped.bam keep5.gff\r\n\r\nisoseq collapse -j 2 --log-level INFO \\\r\n  --do-not-collapse-extra-5exons --max-3p-diff 20 \\\r\n  mapped.bam tight3.gff\r\n<\/code><\/pre>\n
\u5f53\u524d\u5e2e\u52a9\u4fe1\u606f\u4e2d\u7684\u540c\u5916\u663e\u5b50\u4e94\u7aef\u5dee\u5f02\u9ed8\u8ba4\u503c\u4e3a\u4e94\u5341\u78b1\u57fa\uff0c\u4e09\u7aef\u5dee\u5f02\u9ed8\u8ba4\u503c\u4e3a\u4e00\u767e\u78b1\u57fa\uff0c\u5185\u90e8\u6a21\u7cca\u8fde\u63a5\u5bb9\u5dee\u4e3a\u4e94\u78b1\u57fa\u3002\u8fd9\u91cc\u8bb0\u5f55\u5b9e\u9645\u5b89\u88c5\u7248\u672c\u7684\u5e2e\u52a9\u8f93\u51fa\uff0c\u907f\u514d\u628a\u65e7\u6559\u7a0b\u4e2d\u7684\u6570\u503c\u5f53\u6210\u6c38\u4e45\u4e0d\u53d8\u7684\u9ed8\u8ba4\u3002<\/p>\n
\u9ed8\u8ba4\u7ec4\uff0c\u4e5d\u6761\u8bb0\u5f55\u88ab\u653e\u8fdb\u540c\u4e00\u6a21\u578b<\/h2>\n
\u9ed8\u8ba4\u53c2\u6570\u5f97\u5230\u4e24\u4e2a\u6a21\u578b\u3002\u4e0d\u540c\u4f9b\u4f53\u7684\u4e24\u6761\u8bb0\u5f55\u7ec4\u6210\u4e00\u7ec4\uff0c\u5176\u4f59\u4e5d\u6761\u8bb0\u5f55\u5408\u6210\u53e6\u4e00\u7ec4\u3002\u540e\u8005\u5305\u62ec\u4e09\u6761\u5b8c\u6574\u7ed3\u6784\u3001\u4e24\u6761\u7f3a\u9996\u5916\u663e\u5b50\u7684\u7ed3\u6784\u3001\u4e24\u6761\u9996\u7aef\u79fb\u52a8\u7ed3\u6784\u548c\u4e24\u6761\u672b\u7aef\u5ef6\u957f\u7ed3\u6784\u3002<\/p>\n
\u56e0\u6b64\uff0c\u4e5d\u6761\u652f\u6301\u5e76\u4e0d\u610f\u5473\u7740\u4e5d\u6761\u8bb0\u5f55\u90fd\u5177\u6709\u5b8c\u5168\u76f8\u540c\u7684\u5916\u663e\u5b50\u8fb9\u754c\u3002\u5b83\u8868\u793a\u8fd9\u4e9b\u8bb0\u5f55\u5728\u5f53\u524d\u89c4\u5219\u4e0b\u8fdb\u5165\u540c\u4e00\u4e2a\u5f52\u5e76\u7ec4\u3002\u82e5\u628a\u8fd9\u4e2a\u6570\u76f4\u63a5\u5199\u6210\u4e5d\u6761\u5168\u957f\u4e00\u81f4\u8bc1\u636e\uff0c\u5c31\u8d85\u51fa\u4e86\u5b9e\u9645\u8f93\u51fa\u80fd\u8bc1\u660e\u7684\u8303\u56f4\u3002<\/p>\n
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\u9ed8\u8ba4\u7ec4 PB.1.1\r\n\u6210\u5458\u6570         9\r\n\u8f93\u51fa\u5916\u663e\u5b50     2501\u20132900\uff0c4001\u20134400\r\n\u6210\u5458\u6784\u6210       \u5b8c\u6574 3\uff0c\u7f3a\u9996\u5916\u663e\u5b50 2\uff0c\u9996\u7aef\u79fb\u52a8 2\uff0c\u672b\u7aef\u5ef6\u957f 2\r\n<\/code><\/pre>\n
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\n\n\n\n\n\n\n\n
\u8fd0\u884c\u7ec4<\/th>\n\u6a21\u578b\u6570<\/th>\n\u5404\u6a21\u578b\u6210\u5458\u6570<\/th>\n<\/tr>\n<\/thead>\n
\u9ed8\u8ba4\u5f52\u5e76<\/td>\n2<\/td>\n9\uff0c2<\/td>\n<\/tr>\n
\u4fdd\u7559\u4e94\u7aef\u5dee\u5f02<\/td>\n4<\/td>\n5\uff0c2\uff0c2\uff0c2<\/td>\n<\/tr>\n
\u518d\u6536\u7d27\u4e09\u7aef<\/td>\n5<\/td>\n3\uff0c2\uff0c2\uff0c2\uff0c2<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
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\u4e0d\u8981\u88ab\u6587\u4ef6\u540d\u548c\u8ba1\u6570\u5217\u540d\u8bef\u5bfc<\/h2>\n
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