{"id":73217,"date":"2026-11-15T15:03:40","date_gmt":"2026-11-15T07:03:40","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=73217"},"modified":"2026-11-15T15:03:40","modified_gmt":"2026-11-15T07:03:40","slug":"deeptools-missing-zero-strand-heatmap-sort-cpm-practice","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/deeptools-missing-zero-strand-heatmap-sort-cpm-practice\/","title":{"rendered":"deepTools \u5b9e\u8dd1\u590d\u76d8\uff0c\u8865\u96f6\u548c\u6392\u5e8f\u600e\u6837\u6539\u53d8\u540c\u4e00\u6279\u533a\u57df\u7684\u70ed\u56fe"},"content":{"rendered":"
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\u6b63\u94fe\u533a\u7684\u8d77\u70b9\u4e3a 1000\uff0c\u5728\u7532\u8f68\u9053\u4e0a\uff0c\u4ece\u53c2\u8003\u70b9\u4e0a\u6e38\u5230\u4e0b\u6e38\uff0c\u56db\u683c\u4f9d\u6b21\u4e3a\u4e00\u3001\u4e8c\u3001\u4e09\u3001\u56db\u3002\u8d1f\u94fe\u533a\u7684\u57fa\u56e0\u7ec4\u5750\u6807\u662f 2000 \u5230 2200\uff0c\u6211\u4eec\u5728\u53c2\u8003\u70b9\u9644\u8fd1\u6309\u57fa\u56e0\u7ec4\u4ece\u5c0f\u5230\u5927\u7684\u987a\u5e8f\u5199\u5165\u56db\u3001\u4e09\u3001\u4e8c\u3001\u4e00\u3002\u5b9e\u9645\u8f93\u51fa\u4e2d\uff0c\u8d1f\u94fe\u533a\u540c\u6837\u53d8\u6210\u4e00\u3001\u4e8c\u3001\u4e09\u3001\u56db\uff0c\u8bf4\u660e\u65b9\u5411\u5df2\u7ecf\u6309\u533a\u57df\u94fe\u4fe1\u606f\u7edf\u4e00\u3002<\/p>\n

computeMatrix reference-point \\\r\n  --referencePoint TSS \\\r\n  -R regions.bed -S A.bw B.bw \\\r\n  -b 100 -a 100 --binSize 50 \\\r\n  --sortRegions keep -p 2 \\\r\n  -o default.gz \\\r\n  --outFileNameMatrix default.tab \\\r\n  --outFileSortedRegions default.bed\r\n<\/code><\/pre>\n
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\n\n\n\n\n\n\n\n\n
\u533a\u57df\u7c7b\u578b<\/th>\n\u9ed8\u8ba4\u5904\u7406<\/th>\n\u7f3a\u5931\u503c\u8865\u96f6\u540e<\/th>\n<\/tr>\n<\/thead>\n
\u660e\u786e\u5199\u96f6<\/td>\n\u4fdd\u7559\u96f6<\/td>\n\u4ecd\u4e3a\u96f6<\/td>\n<\/tr>\n
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\u534a\u683c\u6709\u4e59\u4fe1\u53f7<\/td>\n\u7b2c\u4e00\u683c\u4e3a 12<\/td>\n\u7b2c\u4e00\u683c\u4e3a 6<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u56e0\u6b64\uff0c\u8865\u96f6\u662f\u5426\u5408\u7406\uff0c\u8981\u56de\u5230\u8f68\u9053\u751f\u6210\u8fc7\u7a0b\u3002\u5982\u679c\u6587\u4ef6\u7701\u7565\u7684\u4f4d\u7f6e\u786e\u5b9a\u8868\u793a\u89c2\u6d4b\u5230\u7684\u96f6\u8986\u76d6\uff0c\u8865\u96f6\u4e0e\u6570\u636e\u542b\u4e49\u53ef\u80fd\u4e00\u81f4\u3002\u5982\u679c\u5b83\u4eec\u4ee3\u8868\u88ab\u8fc7\u6ee4\u3001\u65e0\u6cd5\u8bc4\u4f30\u6216\u672a\u63d0\u4f9b\u7684\u6570\u503c\uff0c\u8865\u96f6\u4f1a\u989d\u5916\u5f15\u5165\u201c\u8fd9\u4e9b\u4f4d\u7f6e\u6ca1\u6709\u4fe1\u53f7\u201d\u7684\u5047\u8bbe\u3002\u53c2\u6570\u5f00\u5173\u53ea\u80fd\u6267\u884c\u5047\u8bbe\uff0c\u65e0\u6cd5\u66ff\u6211\u4eec\u8bc1\u660e\u5047\u8bbe\u6210\u7acb\u3002<\/p>\n
\u6211\u4eec\u540c\u65f6\u4fdd\u7559\u4e86\u7f3a\u5931\u72b6\u6001\u4e0e\u8865\u96f6\u72b6\u6001\u7684\u5b8c\u6574\u77e9\u9635\u3002\u5b9e\u9645\u9879\u76ee\u4e5f\u53ef\u4ee5\u8fd9\u6837\u505a\uff0c\u9009\u53d6\u4e00\u5c0f\u90e8\u5206\u533a\u57df\u8fdb\u884c\u654f\u611f\u6027\u68c0\u67e5\uff0c\u770b\u770b\u7ed3\u8bba\u662f\u5426\u7531\u5927\u91cf\u7f3a\u5931\u4f4d\u7f6e\u9a71\u52a8\u3002\u82e5\u4e24\u79cd\u5904\u7406\u7684\u8d8b\u52bf\u5dee\u5f02\u5f88\u5927\uff0c\u5e94\u5728\u56fe\u6ce8\u548c\u65b9\u6cd5\u4e2d\u4ea4\u4ee3\u6765\u6e90\uff0c\u800c\u4e0d\u662f\u53ea\u4fdd\u7559\u989c\u8272\u66f4\u597d\u770b\u7684\u4e00\u5f20\u3002<\/p>\n
\u56db\u3001\u5220\u9664\u96f6\u503c\u533a\u57df\uff0c\u4f1a\u6539\u53d8\u5e73\u5747\u66f2\u7ebf\u7684\u5206\u6bcd<\/h2>\n
\u9ed8\u8ba4\u77e9\u9635\u4fdd\u7559\u4e03\u4e2a\u533a\u57df\u3002\u542f\u7528\u8df3\u8fc7\u5168\u96f6\u533a\u57df\u540e\uff0c\u672c\u6b21\u8f93\u51fa\u5269\u4e94\u4e2a\uff0c\u660e\u786e\u96f6\u503c\u533a\u4e0e\u5168\u7f3a\u5931\u533a\u90fd\u6ca1\u6709\u4fdd\u7559\u3002\u7f3a\u5931\u503c\u8865\u96f6\u518d\u8df3\u8fc7\u96f6\u503c\uff0c\u4e5f\u5269\u4e94\u4e2a\u3002\u8fd9\u4e2a\u7ed3\u679c\u6765\u81ea\u672c\u7248\u672c\u5728\u672c\u8f93\u5165\u4e0a\u7684\u5b9e\u9645\u884c\u4e3a\uff0c\u4e0d\u5e94\u628a\u53c2\u6570\u540d\u79f0\u7b80\u5355\u7406\u89e3\u4e3a\u201c\u53ea\u5220\u9664\u6587\u4ef6\u91cc\u660e\u786e\u5199\u4e86\u96f6\u7684\u884c\u201d\u3002<\/p>\n
\u7b5b\u9009\u540e\uff0c\u90e8\u5206\u7f3a\u5931\u533a\u4ecd\u5728\uff0c\u56e0\u4e3a\u5b83\u81f3\u5c11\u6709\u975e\u96f6\u5206\u7bb1\u3002\u4e5f\u5c31\u662f\u8bf4\uff0c\u201c\u4e00\u884c\u6709\u6ca1\u6709\u6709\u6548\u4fe1\u53f7\u201d\u548c\u201c\u4e00\u884c\u91cc\u6709\u6ca1\u6709\u7f3a\u5931\u4f4d\u7f6e\u201d\u662f\u4e24\u4e2a\u95ee\u9898\u3002\u8df3\u8fc7\u96f6\u503c\u4e0d\u7b49\u4e8e\u5b8c\u6210\u7f3a\u5931\u503c\u8d28\u63a7\uff0c\u66f4\u4e0d\u7b49\u4e8e\u4fdd\u8bc1\u6bcf\u4e2a\u7559\u4e0b\u7684\u533a\u57df\u90fd\u88ab\u5b8c\u6574\u89c2\u6d4b\u3002<\/p>\n
\u53ef\u4ee5\u7528\u7532\u8f68\u9053\u7b2c\u4e00\u683c\u505a\u4e00\u4e2a\u624b\u5de5\u6838\u5bf9\u3002\u8865\u96f6\u72b6\u6001\u4e0b\uff0c\u4e03\u884c\u6570\u503c\u76f8\u52a0\u4e3a\u5341\u56db\uff0c\u6309\u4e03\u4e2a\u533a\u57df\u5e73\u5747\u5f97\u5230\u4e8c\u3002\u518d\u53bb\u6389\u5168\u96f6\u7684\u4e24\u884c\uff0c\u603b\u548c\u8fd8\u662f\u5341\u56db\uff0c\u6309\u4e94\u4e2a\u533a\u57df\u5e73\u5747\u5374\u53d8\u4e3a\u4e8c\u70b9\u516b\u3002\u8fd9\u662f\u7531\u672c\u6b21\u77e9\u9635\u76f4\u63a5\u8ba1\u7b97\u7684\u7b97\u672f\u793a\u4f8b\uff0c\u5e76\u975e\u53e6\u4e00\u6b21\u771f\u5b9e\u5b9e\u9a8c\u4e2d\u4fe1\u53f7\u589e\u5f3a\u4e86\u56db\u6210\u3002<\/p>\n
\u56e0\u6b64\uff0c\u6bd4\u8f83\u4e0d\u540c\u6761\u4ef6\u7684\u6c47\u603b\u66f2\u7ebf\u65f6\uff0c\u8981\u68c0\u67e5\u5b83\u4eec\u662f\u5426\u9488\u5bf9\u540c\u4e00\u7ec4\u533a\u57df\u3002\u5982\u679c\u6bcf\u4e2a\u6837\u672c\u5404\u81ea\u5220\u9664\u65e0\u4fe1\u53f7\u884c\uff0c\u518d\u5206\u522b\u753b\u5e73\u5747\u503c\uff0c\u56fe\u4e2d\u53d8\u5316\u5c31\u540c\u65f6\u5305\u542b\u4fe1\u53f7\u53d8\u5316\u548c\u533a\u57df\u96c6\u5408\u53d8\u5316\u3002\u66f4\u5bb9\u6613\u89e3\u91ca\u7684\u505a\u6cd5\u662f\u5148\u786e\u5b9a\u9700\u8981\u6bd4\u8f83\u7684\u533a\u57df\u96c6\u5408\uff0c\u628a\u591a\u4e2a\u6837\u672c\u653e\u5165\u540c\u4e00\u77e9\u9635\uff0c\u5e76\u62a5\u544a\u6700\u540e\u4fdd\u7559\u7684\u533a\u57df\u6570\u91cf\u4e0e\u7b5b\u9009\u6761\u4ef6\u3002<\/p>\n
\u4e94\u3001\u6392\u5e8f\u540e\u7b2c\u4e00\u884c\u53d8\u4e86\uff0c\u8eab\u4efd\u4e0d\u80fd\u9760\u4f4d\u7f6e\u731c<\/h2>\n
\u6211\u4eec\u5bf9\u8865\u96f6\u5e76\u7b5b\u9009\u540e\u7684\u540c\u4e00\u4efd\u4e94\u884c\u77e9\u9635\u7ed8\u5236\u4e09\u5f20\u70ed\u56fe\u3002\u7b2c\u4e00\u5f20\u4fdd\u6301\u8f93\u5165\u987a\u5e8f\uff0c\u7b2c\u4e8c\u5f20\u6309\u7532\u8f68\u9053\u7684\u884c\u5747\u503c\u964d\u5e8f\u6392\u5217\uff0c\u7b2c\u4e09\u5f20\u6309\u4e59\u8f68\u9053\u7684\u884c\u5747\u503c\u964d\u5e8f\u6392\u5217\u3002\u6240\u6709\u56fe\u90fd\u4f7f\u7528\u540c\u6837\u7684\u989c\u8272\u8303\u56f4\uff0c\u552f\u4e00\u533a\u522b\u662f\u884c\u987a\u5e8f\u3002<\/p>\n
\u6309\u7532\u6392\u5e8f\uff0c\u7b2c\u4e00\u884c\u662f\u7532\u9ad8\u533a\u3002\u6309\u4e59\u6392\u5e8f\uff0c\u7b2c\u4e00\u884c\u662f\u4e59\u9ad8\u533a\u3002\u540c\u4e00\u5f20\u591a\u6837\u672c\u70ed\u56fe\u5185\uff0c\u4e24\u4e2a\u6837\u672c\u7684\u884c\u4f1a\u5171\u540c\u79fb\u52a8\uff0c\u533a\u57df\u8eab\u4efd\u4ecd\u7136\u5bf9\u9f50\u3002\u5982\u679c\u628a\u4e24\u4e2a\u6837\u672c\u5206\u5f00\u753b\u56fe\u3001\u5404\u81ea\u6392\u5e8f\u540e\u518d\u62fc\u5728\u4e00\u8d77\uff0c\u89c6\u89c9\u4e0a\u540c\u4e00\u9ad8\u5ea6\u7684\u884c\u5c31\u672a\u5fc5\u662f\u540c\u4e00\u4e2a\u533a\u57df\u3002<\/p>\n
\n\n\n\n\n\n\n\n
\u6392\u5217\u65b9\u5f0f<\/th>\n\u7b2c\u4e00\u884c<\/th>\n\u6700\u540e\u4e00\u884c<\/th>\n<\/tr>\n<\/thead>\n
\u4fdd\u6301\u8f93\u5165\u987a\u5e8f<\/td>\n\u6b63\u94fe\u533a<\/td>\n\u90e8\u5206\u7f3a\u5931\u533a<\/td>\n<\/tr>\n
\u6309\u7532\u4fe1\u53f7\u6392\u5e8f<\/td>\n\u7532\u9ad8\u533a<\/td>\n\u90e8\u5206\u7f3a\u5931\u533a<\/td>\n<\/tr>\n
\u6309\u4e59\u4fe1\u53f7\u6392\u5e8f<\/td>\n\u4e59\u9ad8\u533a<\/td>\n\u7532\u9ad8\u533a<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
plotHeatmap -m zeros-skip.gz -o sortA.png \\\r\n  --sortRegions descend --sortUsingSamples 1 \\\r\n  --outFileSortedRegions sortA.bed \\\r\n  --colorMap Blues --zMin 0 --zMax 12\r\n\r\nplotHeatmap -m zeros-skip.gz -o keep.png \\\r\n  --sortRegions keep \\\r\n  --colorMap Blues --zMin 0 --zMax 12\r\n<\/code><\/pre>\n
\u7b2c\u4e00\u6761\u660e\u786e\u6307\u5b9a\u7528\u7b2c\u4e00\u6761\u8f68\u9053\u8ba1\u7b97\u6392\u5e8f\u4f9d\u636e\u3002\u7b2c\u4e8c\u6761\u660e\u786e\u8981\u6c42\u4fdd\u7559\u77e9\u9635\u987a\u5e8f\u3002\u4e0d\u8981\u56e0\u4e3a\u77e9\u9635\u8ba1\u7b97\u65f6\u8bbe\u7f6e\u8fc7\u4fdd\u5e8f\uff0c\u5c31\u8ba4\u4e3a\u7ed8\u56fe\u9636\u6bb5\u4e00\u5b9a\u4e0d\u4f1a\u518d\u6392\u5e8f\u3002\u672c\u6b21\u4fdd\u7559\u6392\u5e8f\u540e\u7684\u533a\u57df\u6e05\u5355\uff0c\u5e76\u6309\u533a\u57df\u540d\u79f0\u6838\u5bf9\u7b2c\u4e00\u884c\u4e0e\u6700\u540e\u4e00\u884c\uff0c\u8ba9\u56fe\u5f62\u53d8\u5316\u80fd\u591f\u4e0e\u6587\u672c\u8bb0\u5f55\u5bf9\u5e94\u3002<\/p>\n
\u53ea\u4fdd\u5b58\u6700\u7ec8\u56fe\u7247\u4e0d\u8db3\u4ee5\u590d\u73b0\u8fd9\u4e00\u6b65\u3002\u81f3\u5c11\u8fd8\u5e94\u4fdd\u5b58\u538b\u7f29\u77e9\u9635\u3001\u7528\u4e8e\u7ed8\u56fe\u7684\u53c2\u6570\u3001\u6392\u5e8f\u540e\u7684\u533a\u57df\u6e05\u5355\uff0c\u4ee5\u53ca\u6837\u672c\u5217\u987a\u5e8f\u3002\u4ee5\u540e\u589e\u52a0\u4e00\u4e2a\u6837\u672c\u65f6\uff0c\u624d\u80fd\u5224\u65ad\u5e94\u8be5\u6cbf\u7528\u539f\u6765\u7684\u6392\u5e8f\u4f9d\u636e\uff0c\u8fd8\u662f\u6709\u610f\u91cd\u65b0\u6392\u5e8f\uff0c\u5e76\u89e3\u91ca\u65b0\u65e7\u56fe\u7247\u4e3a\u4ec0\u4e48\u51fa\u73b0\u4f4d\u7f6e\u53d8\u5316\u3002<\/p>\n
\u516d\u3001\u5bfc\u51fa\u533a\u57df\u6e05\u5355\u540e\uff0c\u8fd8\u8981\u9a8c\u8bc1\u5b83\u80fd\u5426\u5b89\u5168\u590d\u7528<\/h2>\n
\u8fd9\u6b21\u6838\u5bf9\u5bfc\u51fa\u6587\u4ef6\u65f6\uff0c\u9047\u5230\u4e86\u503c\u5f97\u8bb0\u5f55\u7684\u7ec6\u8282\u3002\u6211\u4eec\u8f93\u5165\u7684\u662f\u6ca1\u6709\u5916\u663e\u5b50\u5206\u5757\u7684\u666e\u901a\u516d\u5217\u533a\u95f4\uff0c\u4f46\u5f53\u524d\u6784\u5efa\u5bfc\u51fa\u7684\u6392\u5e8f\u6e05\u5355\u5305\u542b\u66f4\u591a\u5217\u3002\u5176\u4e2d\u4e00\u4e2a\u533a\u57df\u8303\u56f4\u4e3a 3000 \u5230 3200\uff0c\u9644\u52a0\u7684\u5757\u8d77\u70b9\u5b57\u6bb5\u5374\u4e3a 2997\uff0c\u4e0d\u80fd\u76f4\u63a5\u5c06\u8fd9\u7ec4\u9644\u52a0\u5b57\u6bb5\u5f53\u4f5c\u666e\u901a\u5355\u5757 BED12 \u7ed3\u6784\u4f7f\u7528\u3002<\/p>\n
\u672c\u6587\u6ca1\u6709\u636e\u6b64\u63a8\u65ad\u6240\u6709\u7248\u672c\u90fd\u5b58\u5728\u540c\u6837\u95ee\u9898\uff0c\u4e5f\u6ca1\u6709\u4fee\u6539\u539f\u59cb\u5b9e\u6d4b\u8f93\u51fa\u6765\u63a9\u76d6\u5b83\u3002\u56e0\u4e3a\u6211\u4eec\u53ea\u9700\u8981\u6062\u590d\u666e\u901a\u533a\u57df\u7684\u6392\u5217\u987a\u5e8f\uff0c\u811a\u672c\u63d0\u53d6\u524d\u516d\u5217\uff0c\u53e6\u5b58\u4e3a\u987a\u5e8f\u6e05\u5355\uff0c\u518d\u4ea4\u7ed9\u77e9\u9635\u64cd\u4f5c\u5de5\u5177\u6392\u5e8f\u3002\u5b9e\u9645\u8fd0\u884c\u540e\uff0c\u6062\u590d\u51fa\u7684\u533a\u57df\u540d\u79f0\u987a\u5e8f\u4e0e\u76ee\u6807\u987a\u5e8f\u5b8c\u5168\u4e00\u81f4\u3002<\/p>\n
awk 'BEGIN{FS=OFS="\\t"} !\/^#\/ {print $1,$2,$3,$4,$5,$6}' \\\r\n  sortA.bed > sortA.bed6\r\n\r\ncomputeMatrixOperations sort \\\r\n  -m zeros-skip.gz -R sortA.bed6 -o restored.gz\r\n<\/code><\/pre>\n
\u4e0b\u8f7d\u811a\u672c\u7528\u7b49\u4ef7\u7684 Python \u6587\u4ef6\u5904\u7406\u5b8c\u6210\u524d\u516d\u5217\u63d0\u53d6\uff0c\u5e76\u5b9e\u9645\u8fd0\u884c\u540e\u4e00\u6761\u547d\u4ee4\u3002\u8fd9\u91cc\u820d\u5f03\u9644\u52a0\u5217\u662f\u56e0\u4e3a\u8f93\u5165\u5bf9\u8c61\u672c\u6765\u5c31\u6ca1\u6709\u5206\u5757\u7ed3\u6784\u3002\u5982\u679c\u771f\u5b9e\u4efb\u52a1\u9700\u8981\u8f6c\u5f55\u672c\u5916\u663e\u5b50\u4fe1\u606f\uff0c\u4e0d\u80fd\u7167\u642c\u8fd9\u4e2a\u64cd\u4f5c\uff0c\u628a\u5206\u5757\u5217\u5220\u9664\u540e\u4ecd\u58f0\u79f0\u4fdd\u7559\u4e86\u539f\u6765\u7684\u8f6c\u5f55\u672c\u5b9a\u4e49\u3002<\/p>\n
\u4e03\u3001\u4e00\u767e\u4e07\u7684\u8986\u76d6\u6570\u503c\uff0c\u5e76\u4e0d\u8868\u793a\u6d4b\u4e86\u4e00\u767e\u4e07\u6761\u8bfb\u6bb5<\/h2>\n
\u72ec\u7acb\u7684\u8986\u76d6\u5b9e\u9a8c\u5199\u5165\u4e00\u767e\u6761\u5355\u7aef\u6bd4\u5bf9\uff0c\u6bcf\u6761\u957f\u4e94\u5341\u78b1\u57fa\uff0c\u8d77\u70b9\u4e0e\u65b9\u5411\u76f8\u540c\uff0c\u540d\u79f0\u4e0d\u540c\uff0c\u4e14\u6ca1\u6709\u542f\u7528\u91cd\u590d\u8fc7\u6ee4\u3002\u5b83\u4eec\u5168\u90e8\u8986\u76d6\u540c\u4e00\u4e2a\u4e94\u5341\u78b1\u57fa\u5206\u7bb1\u3002\u8fd0\u884c\u4e0d\u5f52\u4e00\u5316\u7684\u8986\u76d6\u8ba1\u7b97\uff0c\u8f93\u51fa\u8be5\u683c\u4e3a\u4e00\u767e\u3002\u6539\u4e3a\u6309\u767e\u4e07\u6bd4\u5bf9\u5f52\u4e00\u5316\u540e\uff0c\u8be5\u683c\u53d8\u4e3a\u4e00\u767e\u4e07\u3002<\/p>\n
\u8ba1\u7b97\u5f88\u76f4\u63a5\uff0c\u4e00\u767e\u6761\u8ba1\u6570\u9664\u4ee5\u4e00\u767e\u6761\u603b\u6bd4\u5bf9\u6240\u5bf9\u5e94\u7684\u767e\u4e07\u5355\u4f4d\uff0c\u5373\u4e00\u767e\u9664\u4ee5\u96f6\u70b9\u96f6\u96f6\u96f6\u4e00\u3002\u8fd9\u4e2a\u4eba\u4e3a\u4f8b\u5b50\u8bf4\u660e\u8f68\u9053\u6570\u503c\u5e26\u6709\u5355\u4f4d\uff0c\u8f83\u5927\u7684\u5f52\u4e00\u5316\u503c\u53ef\u80fd\u53ea\u662f\u5206\u6bcd\u8f83\u5c0f\uff0c\u4e0d\u610f\u5473\u7740\u6d4b\u5e8f\u91cf\u975e\u5e38\u5927\uff0c\u4e5f\u4e0d\u80fd\u5355\u72ec\u8bc1\u660e\u5bcc\u96c6\u53ef\u4fe1\u3002<\/p>\n
bamCoverage -b fixture.bam -o raw.bedgraph \\\r\n  --outFileFormat bedgraph --binSize 50 \\\r\n  --normalizeUsing None --exactScaling -p 2\r\n\r\nbamCoverage -b fixture.bam -o cpm.bedgraph \\\r\n  --outFileFormat bedgraph --binSize 50 \\\r\n  --normalizeUsing CPM --exactScaling -p 2\r\n<\/code><\/pre>\n
\u6211\u4eec\u6545\u610f\u8ba9\u8fd9\u4e9b\u6bd4\u5bf9\u5177\u6709\u76f8\u540c\u4f4d\u7f6e\uff0c\u76ee\u7684\u662f\u8ba9\u6570\u503c\u53ef\u4ee5\u7acb\u5373\u6838\u5bf9\uff0c\u4e0d\u662f\u5728\u63d0\u51fa\u771f\u5b9e\u6570\u636e\u4fdd\u7559\u91cd\u590d\u7684\u5efa\u8bae\u3002\u771f\u5b9e\u6587\u5e93\u7684\u91cd\u590d\u5904\u7406\u5e94\u8003\u8651\u5b9e\u9a8c\u7c7b\u578b\u3001\u6587\u5e93\u590d\u6742\u5ea6\u53ca\u4e0a\u6e38\u6d41\u7a0b\uff0c\u5e76\u5728\u6bd4\u8f83\u6837\u672c\u65f6\u4fdd\u6301\u4e00\u81f4\u3002\u672c\u4f8b\u4e5f\u6ca1\u6709\u53cc\u7aef\u7247\u6bb5\u3001\u8f93\u5165\u5bf9\u7167\u6216\u5916\u6e90\u53c2\u7167\uff0c\u4e0d\u80fd\u628a\u5176\u8ba1\u6570\u5355\u4f4d\u63a8\u5e7f\u6210\u6240\u6709\u5b9e\u9a8c\u4e2d\u7684\u5206\u5b50\u6570\u91cf\u3002<\/p>\n
\u516b\u3001\u4ece\u4e00\u5f20\u80fd\u753b\u51fa\u7684\u56fe\uff0c\u8d70\u5411\u4e00\u5f20\u80fd\u89e3\u91ca\u7684\u56fe<\/h2>\n
\u8fd9\u7ec4\u5b9e\u9a8c\u7684\u7ecf\u9a8c\u662f\uff0c\u7ed8\u56fe\u95ee\u9898\u53ef\u4ee5\u5206\u5c42\u6392\u67e5\u3002\u5148\u786e\u8ba4\u533a\u57df\u548c\u65b9\u5411\uff0c\u89e3\u91ca\u6a2a\u8f74\u3002\u518d\u786e\u8ba4\u8f68\u9053\u7684\u751f\u6210\u65b9\u6cd5\uff0c\u89e3\u91ca\u6570\u503c\u5355\u4f4d\u3002\u7136\u540e\u68c0\u67e5\u7f3a\u5931\u4e0e\u96f6\u503c\uff0c\u89e3\u91ca\u5206\u7bb1\u5747\u503c\u3002\u6700\u540e\u6838\u5bf9\u7b5b\u9009\u3001\u6392\u5e8f\u548c\u8272\u6807\uff0c\u89e3\u91ca\u56fe\u4e2d\u533a\u57df\u96c6\u5408\u4e0e\u989c\u8272\u5dee\u5f02\u3002\u524d\u4e00\u5c42\u6ca1\u6709\u786e\u5b9a\uff0c\u540e\u4e00\u5c42\u7684\u7f8e\u5316\u5f88\u96be\u8865\u6551\u3002<\/p>\n
deepTools \u7684\u4f18\u52bf\u662f\u628a\u8986\u76d6\u8f68\u9053\u3001\u6570\u503c\u77e9\u9635\u548c\u56fe\u5f62\u8fde\u63a5\u8d77\u6765\uff0c\u80fd\u591f\u4fdd\u7559\u9002\u5408\u590d\u67e5\u7684\u4e2d\u95f4\u6587\u4ef6\u3002\u9650\u5236\u662f\u8fd9\u4e9b\u8fde\u63a5\u4f9d\u8d56\u660e\u786e\u7684\u8f93\u5165\u8bed\u4e49\u3002\u70ed\u56fe\u7684\u805a\u96c6\u6216\u5206\u79bb\u53ef\u4ee5\u5e2e\u52a9\u53d1\u73b0\u6a21\u5f0f\uff0c\u5374\u4e0d\u80fd\u66ff\u4ee3\u91cd\u590d\u6837\u672c\u7684\u7edf\u8ba1\u68c0\u9a8c\u3002\u672c\u6b21\u53ea\u6784\u9020\u4e24\u6761\u8f68\u9053\uff0c\u6ca1\u6709\u4f30\u8ba1\u751f\u7269\u5b66\u53d8\u5f02\uff0c\u4e5f\u6ca1\u6709\u8ba1\u7b97\u663e\u8457\u5dee\u5f02\u533a\u57df\u3002<\/p>\n
\u4e0b\u8f7d\u672c\u7ec4\u4e09\u7bc7\u590d\u73b0\u811a\u672c\u4e0e\u5b9e\u6d4b\u8bb0\u5f55<\/a>\uff0c\u5728\u6709 Docker \u7684 Linux \u73af\u5883\u8fd0\u884c\u672c\u5de5\u5177\u76ee\u5f55\u4e0b\u7684\u811a\u672c\uff0c\u5373\u53ef\u91cd\u5efa\u8f68\u9053\u3001\u77e9\u9635\u548c\u4e09\u5f20\u70ed\u56fe\u3002\u672c\u6b21\u56fa\u5b9a\u4f7f\u7528 3.5.6 \u73af\u5883\uff0c\u5b9e\u9645 Python \u4e3a 3.12.8\uff0c\u8bfb\u53d6\u8f68\u9053\u4e0e\u6bd4\u5bf9\u6587\u4ef6\u7684\u4f9d\u8d56\u7248\u672c\u4e5f\u5199\u5165\u7ed3\u679c\u3002\u56fa\u5b9a\u7248\u672c\u662f\u4e3a\u4e86\u590d\u73b0\u672c\u6b21\u884c\u4e3a\uff0c\u4e0d\u8868\u793a\u5b83\u662f\u5f53\u524d\u6700\u65b0\u7248\u672c\u3002<\/p>\n
python3 run.py output\r\n<\/code><\/pre>\n
\u5b9a\u4e49\u4e0e\u53c2\u6570\u53ef\u4ee5\u8fdb\u4e00\u6b65\u67e5\u9605 computeMatrix \u6587\u6863<\/a>\u3001plotHeatmap \u6587\u6863<\/a>\u3001\u77e9\u9635\u64cd\u4f5c\u6587\u6863<\/a> \u548c bamCoverage \u6587\u6863<\/a>\u3002\u672c\u6587\u6240\u5217\u6570\u503c\u4e0e\u987a\u5e8f\u6765\u81ea\u672c\u6b21\u53ef\u4e0b\u8f7d\u8bb0\u5f55\u3002<\/p>\n
\u5f53\u8f68\u9053\u5355\u4f4d\u3001\u533a\u57df\u96c6\u5408\u548c\u7ed8\u56fe\u53e3\u5f84\u90fd\u6838\u5bf9\u6e05\u695a\u540e\uff0c\u82e5\u9700\u6269\u5c55\u5230\u591a\u6837\u672c\u7684\u5927\u6279\u91cf\u4fe1\u53f7\u8ba1\u7b97\uff0c\u53ef\u643a\u5e26\u6837\u672c\u6570\u91cf\u3001\u8f68\u9053\u89c4\u6a21\u548c\u590d\u73b0\u53c2\u6570\uff0c\u901a\u8fc7\u4e91\u751f\u4fe1\u751f\u7269\u5206\u6790\u670d\u52a1\u5668\u670d\u52a1<\/a>\u8bc4\u4f30\u73af\u5883\u4e0e\u4efb\u52a1\u5b89\u6392\u3002<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"
\u5b9e\u9645\u8fd0\u884c deepTools \u7684\u77e9\u9635\u3001\u70ed\u56fe\u548c\u8986\u76d6\u5de5\u5177\uff0c\u6838\u5bf9\u8d1f\u94fe\u65b9\u5411\u3001\u90e8\u5206\u7f3a\u5931\u8865\u96f6\u3001\u7b5b\u9009\u540e\u7684\u5206\u6bcd\u3001\u6392\u5e8f\u987a\u5e8f\u53ca CPM \u7684\u6570\u503c\u5355\u4f4d\u3002<\/p>\n","protected":false},"author":1,"featured_media":73216,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_post_was_ever_published":false},"categories":[49],"tags":[1393,1401,1400,1402],"class_list":["post-73217","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-software","tag-atac-seq","tag-chip-seq","tag-deeptools","tag-1402"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2026\/11\/deeptools-missing-zero-strand-heatmap-sort-cpm-practice-guide.png?fit=1200%2C840&ssl=1","_links":{"self":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/73217","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/comments?post=73217"}],"version-history":[{"count":1,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/73217\/revisions"}],"predecessor-version":[{"id":73221,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/posts\/73217\/revisions\/73221"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/media\/73216"}],"wp:attachment":[{"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/media?parent=73217"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/categories?post=73217"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.biocloudservice.com\/wordpress\/wp-json\/wp\/v2\/tags?post=73217"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}