{"id":23883,"date":"2024-01-09T17:31:48","date_gmt":"2024-01-09T09:31:48","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23883"},"modified":"2024-01-09T17:31:49","modified_gmt":"2024-01-09T09:31:49","slug":"%e5%bf%ab%e6%9d%a5%e5%ad%a6%ef%bc%81%e4%bd%a0%e4%b8%8d%e7%9f%a5%e9%81%93%e7%9a%84tss%e5%af%8c%e9%9b%86%e7%83%ad%e5%9b%be%e4%b8%ad%e7%9a%84%e5%b0%8f%e7%bb%86%e8%8a%82","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=23883","title":{"rendered":"\u5feb\u6765\u5b66\uff01\u4f60\u4e0d\u77e5\u9053\u7684TSS\u5bcc\u96c6\u70ed\u56fe\u4e2d\u7684\u5c0f\u7ec6\u8282"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u6709\u70b9\u5fe7\u4f24\uff0c\u4e3a\u4ec0\u4e48\u8bba\u6587\u91cc\u9762\u7684TSS\u5bcc\u96c6\u56fe\u90a3\u4e48\u7f8e\u89c2\uff0c\u5c0f\u679c\u7684\u5374\u7565\u663e\u4e11\u964b\u5462<\/p>\n

\u4e0b\u9762\u662f\u8bba\u6587\u4e2d\u7684TSS\u5bcc\u96c6\u56fe\uff0c\u5927\u5bb6\u6b23\u8d4f\u4e00\u4e0b<\/p>\n

<\/p>\n

\u4e0b\u9762\u5462\u5219\u662f\u76f8\u6bd4\u8d77\u6765\u7565\u663e\u4e0d\u884c\u7684\u5c0f\u679c\u505a\u7684TSS\u5bcc\u96c6\u56fe\uff0c\u5927\u5bb6\u6b23\u8d4f\u4e00\u4e0b<\/p>\n

<\/p>\n

\u4e0d\u6bd4\u4e0d\u77e5\u9053\uff0c\u4e00\u6bd4\u5413\u4e00\u8df3\uff01<\/p>\n

\u5c0f\u679c\u505a\u7684\u56fe\u91cc\u9762\u6709\u5f88\u591a\u7684\u201d\u9ed1\u7ebf\u201d\uff0c\u5341\u5206\u5f71\u54cd\u7f8e\u89c2!<\/p>\n

\u8fd9\u53ef\u600e\u4e48\u529e\u5462\uff0c\u5c0f\u679c\u8d76\u7d27\u53c8\u53bb\u4ed4\u7ec6\u9605\u8bfb\u4e86deeptools\u7684\u5e2e\u52a9\u6587\u6863<\/p>\n

–plotType {lines,fill,se,std}<\/p>\n

“lines” will plot the profile line based on the<\/p>\n

average type selected. “fill” fills the region between<\/p>\n

zero and the profile curve. The fill in color is semi<\/p>\n

transparent to distinguish different profiles. “se”<\/p>\n

and “std” color the region between the profile and the<\/p>\n

standard error or standard deviation of the data.<\/p>\n

(default: lines)<\/p>\n

–sortUsingSamples SORTUSINGSAMPLES [SORTUSINGSAMPLES …]<\/p>\n

List of sample numbers (order as in matrix), which are<\/p>\n

used by –sortUsing for sorting. If no value is set,<\/p>\n

it uses all samples. Example: –sortUsingSamples 1 3<\/p>\n

(default: None)<\/p>\n

–linesAtTickMarks Draw dashed lines from all tick marks through the<\/p>\n

heatmap. This is then similar to the dashed line draw<\/p>\n

at region bounds when using a reference point and<\/p>\n

–sortUsing region_length (default: False)<\/p>\n

–clusterUsingSamples CLUSTERUSINGSAMPLES [CLUSTERUSINGSAMPLES …]<\/p>\n

List of sample numbers (order as in matrix), that are<\/p>\n

used for clustering by –kmeans or –hclust if not<\/p>\n

given, all samples are taken into account for<\/p>\n

clustering. Example: –ClusterUsingSamples 1 3<\/p>\n

(default: None)<\/p>\n

–averageTypeSummaryPlot {mean,median,min,max,std,sum}<\/p>\n

Define the type of statistic that should be plotted in<\/p>\n

the summary image above the heatmap. The options are:<\/p>\n

“mean”, “median”, “min”, “max”, “sum” and “std”.<\/p>\n

(default: mean)<\/p>\n

–missingDataColor MISSINGDATACOLOR<\/p>\n

If –missingDataAsZero was not set, such cases will be<\/p>\n

colored in black by default. Using this parameter, a<\/p>\n

different color can be set. A value between 0 and 1<\/p>\n

will be used for a gray scale (black is 0). For a list<\/p>\n

of possible color names see: http:\/\/packages.python.or<\/p>\n

g\/ete2\/reference\/reference_svgcolors.html. Other<\/p>\n

colors can be specified using the #rrggbb notation.<\/p>\n

(default: black)<\/p>\n

–colorNumber COLORNUMBER<\/p>\n

N.B., –colorList is required for an effect. This<\/p>\n

controls the number of transitions from one color to<\/p>\n

the other. If –colorNumber is the number of colors in<\/p>\n

–colorList then there will be no transitions between<\/p>\n

the colors. (default: 256)<\/p>\n

–heatmapHeight HEATMAPHEIGHT<\/p>\n

Plot height in cm. The default for the heatmap height<\/p>\n

is 28. The minimum value is 3 and the maximum is 100.<\/p>\n

(default: 28)<\/p>\n

–heatmapWidth HEATMAPWIDTH<\/p>\n

Plot width in cm. The default value is 4 The minimum<\/p>\n

value is 1 and the maximum is 100. (default: 4)<\/p>\n

\u4e0a\u9762\u51e0\u4e2a\u53c2\u6570\u662f\u5c0f\u679c\u4ed4\u7ec6\u9605\u8bfb\u4e4b\u540e\u53d1\u73b0\u6709\u53ef\u80fd\u5f71\u54cd\u201c\u9ed1\u7ebf\u201d\u7684\u5173\u952e\u53c2\u6570\uff0c\u4e0d\u8fc7\u5c0f\u679c\u611f\u89c9\u4e00\u4e2a\u4e00\u4e2a\u53bb\u5b9e\u9a8c\u592a\u9ebb\u70e6\u4e86\uff0c\u53ea\u80fd\u53bb\u6c42\u52a9\u4e07\u80fd\u7684\u5ea6\u5a18\uff0c\u91cc\u9762\u6709\u5c0f\u4f19\u4f34\u8bf4\u51fa\u73b0\u9ed1\u7ebf\u662f\u56e0\u4e3a\u5728\u4f7f\u7528computeMatrix\u5f62\u6210\u77e9\u9635\u6587\u4ef6\u6ca1\u6709\u6dfb\u52a0\u53c2\u6570–missingDataAsZero\uff01\u5c0f\u679c\u6ca1\u6709\u60f3\u5230\u662f\u56e0\u4e3a\u5f62\u6210\u77e9\u9635\u6587\u4ef6\u7684\u95ee\u9898\uff0c\u5e78\u4e8f\u5c0f\u679c\u6ca1\u6709\u4e00\u4e2a\u4e2a\u53c2\u6570\u5b9e\u9a8c\uff0c\u90a3\u6015\u4e0d\u662f\u767d\u767d\u6d6a\u8d39\u65f6\u95f4\uff01<\/p>\n

\u5728\u4e86\u89e3\u5230\u4e86\u95ee\u9898\u6240\u5728\u4e4b\u540e\uff0c\u5c0f\u679c\u5feb\u9a6c\u52a0\u97ad\u53bb\u5b9e\u9a8c\u4e86\u4e00\u4e0b\uff0c\u4e0b\u9762\u662f\u5c0f\u679c\u7684\u4f7f\u7528computeMatrix\u547d\u4ee4\u5f62\u6210\u77e9\u9635\u6587\u4ef6\u7684\u53c2\u6570\uff1a<\/p>\n

computeMatrix reference-point –referencePoint TSS -p 15 -b 10000 -a 10000 -R gene.bed -S test.bw –skipZeros –missingDataAsZero -o test_TSS.gz –outFileSortedRegions test_genes.bed<\/p>\n

\u4e0b\u9762\u662f\u53c2\u6570\u7684\u89e3\u91ca\uff1a<\/p>\n

reference-point # \u9009\u62e9\u6a21\u5f0f<\/p>\n

-p 15 # \u7ebf\u7a0b\u6570<\/p>\n

–referencePoint TSS # \u9009\u62e9\u53c2\u8003\u70b9\uff0c\u8fd8\u53ef\u4ee5\u9009\u62e9TES, center<\/p>\n

-b 10000 -a 10000 # \u611f\u5174\u8da3\u7684\u533a\u57df\uff0c-b\u4e0a\u6e38\uff0c-a\u4e0b\u6e38<\/p>\n

-R # \u57fa\u56e0\u6ce8\u91ca\u4fe1\u606f<\/p>\n

-S # \u63d0\u4f9b\u7684 bigwig \u6587\u4ef6<\/p>\n

–skipZeros # \u662f\u5426\u5305\u542b\u96f6\u5206\u533a\u57df<\/p>\n

–missingDataAsZero # \u4e0d\u663e\u793a0\u7684\u6570\u636e<\/p>\n

\u4e0b\u9762\u662fmissingDataAsZero \u53c2\u6570\u7684\u5b98\u65b9\u89e3\u91ca\uff0c\u5927\u5bb6\u53ef\u4ee5\u8bd5\u7740\u7406\u89e3\u4e00\u4e0b\u55f7<\/p>\n

If set, missing data (NAs) will be treated as zeros.<\/p>\n

The default is to ignore such cases, which will be<\/p>\n

depicted as black areas in a heatmap. (see the<\/p>\n

–missingDataColor argument of the plotHeatmap command<\/p>\n

for additional options). (default: False)<\/p>\n

\u4e0b\u9762\u6765\u6b23\u8d4f\u4e00\u4e0b\u5c0f\u679c\u65b0\u7684TSS\u5bcc\u96c6\u70ed\u56fe\u5427<\/p>\n

<\/p>\n

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\u4eca\u5929\u7684\u5173\u4e8eTSS\u5bcc\u96c6\u70ed\u56fe\u7684\u5c0f\u7ec6\u8282\u5b66\u4e60\u5c31\u5230\u8fd9\u91cc\u5566\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u627e\u5c0f\u679c\u8ba8\u8bba\u54e6\uff0c\u6211\u4eec\u660e\u5929\u89c1\u54af~<\/p>\n","protected":false},"excerpt":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u6709\u70b9\u5fe7\u4f24\uff0c\u4e3a\u4ec0\u4e48\u8bba\u6587\u91cc\u9762\u7684TSS\u5bcc\u96c6\u56fe\u90a3\u4e48\u7f8e\u89c2\uff0c\u5c0f\u679c\u7684\u5374\u7565\u663e\u4e11\u964b\u5462 \u4e0b\u9762\u662f\u8bba\u6587\u4e2d\u7684TSS\u5bcc\u96c6\u56fe\uff0c\u5927\u5bb6\u6b23 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23883"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=23883"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23883\/revisions"}],"predecessor-version":[{"id":23889,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/23883\/revisions\/23889"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=23883"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=23883"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=23883"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}