{"id":2116,"date":"2025-10-11T18:58:14","date_gmt":"2025-10-11T10:58:14","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=2116"},"modified":"2025-12-14T11:58:22","modified_gmt":"2025-12-14T03:58:22","slug":"%e5%a6%82%e4%bd%95%e7%bb%98%e5%88%b6%e4%b8%80%e4%b8%aa%e4%b8%8d%e6%99%ae%e9%80%9a%e7%9a%84%e5%9f%ba%e5%9b%a0%e7%bb%84circos%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/10\/11\/%e5%a6%82%e4%bd%95%e7%bb%98%e5%88%b6%e4%b8%80%e4%b8%aa%e4%b8%8d%e6%99%ae%e9%80%9a%e7%9a%84%e5%9f%ba%e5%9b%a0%e7%bb%84circos%e5%9b%be\/","title":{"rendered":"\u5982\u4f55\u7ed8\u5236\u4e00\u4e2a\u201d\u4e0d\u666e\u901a\u201c\u7684\u57fa\u56e0\u7ec4Circos\u56fe"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"2116\" class=\"elementor elementor-2116\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-cc47c3e e-flex e-con-boxed e-con e-parent\" data-id=\"cc47c3e\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-b23bef5 elementor-widget elementor-widget-heading\" data-id=\"b23bef5\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">1. \u524d\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c559625 elementor-widget elementor-widget-text-editor\" data-id=\"c559625\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u57fa\u56e0\u7ec4Circos\u56fe\u57fa\u672c\u4e0a\u662f\u6bcf\u4e2a\u57fa\u56e0\u7ec4\u7814\u7a76\u5fc5\u5907\u7684\uff0c\u4f46\u662f\u4f18\u96c5\u7684\u7ed8\u5236\u4e00\u4e2a\u201c\u4e0d\u666e\u901a\u7684Circos\u56fe\u5462\u201d\uff1f\u6240\u4ee5\u4eca\u5929\u6765\u8bb0\u5f55\u4e00\u4e0b\u81ea\u5df1\u7ed8\u5236\u57fa\u56e0\u7ec4Circos\u56fe\u7684\u8fc7\u7a0b\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fa77f38 elementor-widget elementor-widget-heading\" data-id=\"fa77f38\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">2. \u6570\u636e\u51c6\u5907<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fd429c8 elementor-widget elementor-widget-text-editor\" data-id=\"fd429c8\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8fd9\u90e8\u5206\u6709\u4e00\u4e9b\u539f\u59cb\u7ed3\u679c\u53ef\u4ee5\u901a\u8fc7\u4e0d\u540c\u7684\u8f6f\u4ef6\u5f97\u5230\uff0c\u91cd\u590d\u5e8f\u5217\u7684gff\u6587\u4ef6\u6211\u901a\u8fc7EDTA\uff0c\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\u6570\u636e\u6211\u901a\u8fc7nf-core\/rna-seq\uff0c\u5171\u7ebf\u6027\u6211\u901a\u8fc7jcvi<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8083212 elementor-widget elementor-widget-text-editor\" data-id=\"8083212\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\uff081\uff09\u57fa\u56e0\u7ec4\u7684\u957f\u5ea6\u4fe1\u606f<\/p><p>\uff082\uff09GC\u542b\u91cf<\/p><p>\uff083\uff09\u57fa\u56e0\u5bc6\u5ea6<\/p><p>\uff084\uff09\u91cd\u590d\u5e8f\u5217\u5bc6\u5ea6<\/p><p>\uff085\uff09DNA\u53cd\u8f6c\u5ea7\u5b50\u5bc6\u5ea6<\/p><p>\uff086\uff09Copia\u5bc6\u5ea6<\/p><p>\uff087\uff09Gypsy\u5bc6\u5ea6<\/p><p>\uff088\uff09LTR\u5bc6\u5ea6<\/p><p>\uff089\uff09\u5171\u7ebf\u6027Link<\/p><p>\uff0810\uff09\u57fa\u56e0\u8868\u8fbe\u91cf\u5bc6\u5ea6<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f0dc02a elementor-widget elementor-widget-code-highlight\" data-id=\"f0dc02a\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>## \u8ba1\u7b97\u67d3\u8272\u4f53\u957f\u5ea6\nseqtk comp  genome.fasta|awk '{print $1\"\\t\"$2}' > genome.len\n## \u751f\u6210\u67d3\u8272\u4f53\u6587\u4ef6 7\u5217\nawk '{print \"chr\\t-\\t\"$1\"\\t\"$1\"\\t0\\t\"$2\"\\tchr\"NR}' genome.len > Sind_karyotype.txt\n## \u751f\u6210\u7a97\u53e3\u6587\u4ef6\uff0c \u7a97\u53e3\u5927\u5c0f50Kb\nbedtools  makewindows -w 50000 -g  genome.len > genome.window.bed\n## \u8ba1\u7b97\u57fa\u56e0\u5bc6\u5ea6\nbedtools intersect  -a genome.window.bed -b Sind.bed -c -F 0.1  > Sind_genecount.txt\n## \u8ba1\u7b97\u6bcf\u4e2a\u7a97\u53e3\u5e73\u5747GC\u542b\u91cf\nseqtk subseq genome.fasta  genome.window.bed  > genome.window.fasta\nseqtk comp  genome.window.fasta |awk '{print $1 \"\\t\" ($4+$5)\/($3+$4+$5+$6) } ' |awk -F \":|-\" '{print $1\"\\t\"$2\"\\t\"$3\"\\t\"$4}'> Sind_gc.txt\n## \u8ba1\u7b97\u6bcf\u4e2a\u7a97\u53e3\u91cd\u590d\u5e8f\u5217\u542b\u91cf\ngrep \"LTR\" ..\/Anno\/quarTeT.genome.filled.fasta.mod.EDTA.intact.gff3 > quarTeT.genome.filled.fasta.repeat.LTR.gff\ngrep \"Copia\" ..\/Anno\/quarTeT.genome.filled.fasta.mod.EDTA.intact.gff3 > quarTeT.genome.filled.fasta.repeat.Copia.gff\ngrep \"DNA\" ..\/Anno\/quarTeT.genome.filled.fasta.mod.EDTA.intact.gff3 > quarTeT.genome.filled.fasta.repeat.DNA.gff\ngrep \"Gypsy\" ..\/Anno\/quarTeT.genome.filled.fasta.mod.EDTA.intact.gff3 > quarTeT.genome.filled.fasta.repeat.Gypsy.gff\nbedtools coverage -a  genome.window.bed -b  quarTeT.genome.filled.fasta.repeat.Copia.gff |awk '{print $1 \"\\t\" $2 \"\\t\" $3 \"\\t\" $7}' > Repeat_Copia.txt\nbedtools coverage -a  genome.window.bed -b  quarTeT.genome.filled.fasta.repeat.DNA.gff |awk '{print $1 \"\\t\" $2 \"\\t\" $3 \"\\t\" $7}' > Repeat_DNA.txt\nbedtools coverage -a  genome.window.bed -b  quarTeT.genome.filled.fasta.repeat.Gypsy.gff |awk '{print $1 \"\\t\" $2 \"\\t\" $3 \"\\t\" $7}' > Repeat_Gypsy.txt\nbedtools coverage -a  genome.window.bed -b  quarTeT.genome.filled.fasta.repeat.LTR.gff |awk '{print $1 \"\\t\" $2 \"\\t\" $3 \"\\t\" $7}' > Repeat_LTR.txt\nbedtools coverage -a  genome.window.bed -b  repeat.gff |awk '{print $1 \"\\t\" $2 \"\\t\" $3 \"\\t\" $7}' > Repeat.txt\n## \u57fa\u4e8ejcvi\u7ed3\u679c\u751f\u6210\u5171\u7ebf\u6027link\u6587\u4ef6\nperl get_jcvi_block.pl  Sind.bed  Sind.Sind.anchors 8  >  Sind_links.txt\n## \u8ba1\u7b97\u57fa\u56e0\u8868\u8fbe\u91cf\u5bc6\u5ea6\npython merge_tpm_to_bed.py -b Prunus_pedunculata_Chr_gene.bed -t salmon.merged.gene_tpm.tsv -o Prunus_pedunculata_Chr_gene_TPM.bed\nbedtools map -a \/home\/majunpeng\/sda2\/Biantao_Sequence_data\/Circos\/genome.window.bed -b \/home\/majunpeng\/sda2\/Biantao_Sequence_data\/Circos\/Prunus_pedunculata_Chr_gene_TPM.bed -c 5 -o sum -null 0 > \/home\/majunpeng\/sda2\/Biantao_Sequence_data\/Circos\/gene_expression_sum_in_windows.bed<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fe572a0 elementor-widget elementor-widget-heading\" data-id=\"fe572a0\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">3. \u7ed8\u5236Circos\u56fe<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-610d613 elementor-widget elementor-widget-text-editor\" data-id=\"610d613\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u51c6\u5907\u4e09\u4e2a\u914d\u7f6e\u6587\u4ef6\uff081\uff09circos.conf\uff0c\u4e3b\u914d\u7f6e\u6587\u4ef6\uff082\uff09ideogram.conf\uff0c\u67d3\u8272\u4f53\u9aa8\u67b6\u914d\u7f6e\u6587\u4ef6\uff083\uff09ticks.conf\uff0c\u67d3\u8272\u4f53\u9aa8\u67b6\u523b\u5ea6\u6587\u4ef6\u5939<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-70fb774 elementor-widget elementor-widget-code-highlight\" data-id=\"70fb774\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp><ideogram>\r\n\r\n##\u8bbe\u5b9a\u67d3\u8272\u4f53\u95f4\u7684\u7a7a\u9699\u5927\u5c0f\r\n\r\n<spacing>\r\ndefault = 0.005r #\u8bbe\u7f6e\u5708\u56fe\u4e2d\u67d3\u8272\u4f53\u4e4b\u95f4\u7684\u7a7a\u9699\u5927\u5c0f\uff0c\u4ee5\u4e0b\u8bbe\u7f6e\u4e3a\u6bcf\u4e2a\u7a7a\u9699\u5927\u5c0f\u4e3a\u5468\u957f\u76841%\r\n\r\n<\/spacing>\r\n\r\nradius = 0.8r #\u8bbe\u5b9a ideograms \u7684\u4f4d\u7f6e\uff0c\u4ee5\u4e0b\u8bbe\u5b9a ideograms \u5728\u79bb\u5706\u5fc3\u7684 90% \u5904\r\nthickness = 15p #\u8bbe\u5b9a ideograms \u7684\u539a\u5ea6\u4e3a10p\r\nfill = yes #\u8bbe\u5b9aideograms\u662f\u5426\u586b\u5145\u989c\u8272\u3002\r\n\r\nstroke_color = dgrey #\u8bbe\u7f6e\u8f6e\u5ed3\u989c\u8272\r\nstroke_thickness = 1p #\u8bbe\u7f6e\u8f6e\u5ed3\u539a\u5ea6\r\n\r\nshow_label = yes #\u8bbe\u5b9a\u662f\u5426\u663e\u793alabel, \u5bf9\u5e94\u7740karyotype\u6587\u4ef6\u7684\u7b2c4\u5217\u3002\r\nlabel_radius = 1.07r #\u8bbe\u5b9a label \u7684\u4f4d\u7f6e\r\nlabel_font = default #\u8bbe\u7f6e\u5b57\u4f53\r\nlabel_size = 40p #\u8bbe\u5b9alabel\u7684\u5b57\u4f53\u5927\u5c0f\r\nlabel_parallel = no #\u8bbe\u5b9alabel\u7684\u6587\u5b57\u65b9\u5411\uff0cyes\u8868\u793a\u5e73\u884c\u4e8e\u67d3\u8272\u4f53\u3002\r\n\r\n<\/ideogram>\r\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4ceb07e elementor-widget elementor-widget-code-highlight\" data-id=\"4ceb07e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp><ticks>\r\n\r\nradius = 1r  #\u8bbe\u5b9a ticks \u7684\u4f4d\u7f6e\r\ncolor = vdred # \u8bbe\u5b9a ticks \u7684\u989c\u8272\r\nthickness = 2p # \u8bbe\u5b9a ticks \u7684\u539a\u5ea6\r\n\r\nmultiplier = 1e-6 # \u8bbe\u5b9a ticks label \u7684\u503c\u7684\u8ba1\u7b97\u3002\u5c06\u8be5\u523b\u5ea6\u5bf9\u5e94\u4f4d\u7f6e\u7684\u503c * multiplier \u5f97\u5230\u5708\u56fe\u4e0a\u7684label \u503c\u3002\r\norientation = out # \u8bbe\u5b9aticks\u5411\u5916\u8fd8\u662f\u5411\u5185 \u53ef\u4ee5\u8bbe\u7f6e\u503c\u4e3a out \u548c in\r\nformat = %d # label\u503c\u7684\u683c\u5f0f\u5316\u65b9\u5f0f\u3002%d \u8868\u793a\u7ed3\u679c\u4e3a\u6574\u6570\uff1b%f \u7ed3\u679c\u4e3a\u6d6e\u70b9\u6570\uff1b %.1f \u7ed3\u679c\u4e3a\u5c0f\u6570\u70b9\u540e\u4fdd\u75591\u4f4d.\r\n\r\n<tick>\r\nspacing = 10u # \u8bbe\u7f6e\u6bcf\u4e2a\u523b\u5ea6\u4ee3\u8868\u7684\u957f\u5ea6\u3002\r\nsize = 15p  # \u8bbe\u7f6e tick \u7684\u957f\u5ea6\r\n\r\nshow_label = yes #\u8bbe\u7f6e\u5c55\u793a ticks label\u3002\r\nlabel_size = 20p #\u8bbe\u7f6e ticks label \u7684\u5b57\u4f53\u5927\u5c0f\r\nlabel_offset = 5p #\u8bbe\u7f6e ticks label \u79bb ticks \u7684\u8ddd\u79bb\r\nformat = %d\r\n<\/tick>\r\n\r\n<\/ticks>\r\n\r\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-a718abd elementor-widget elementor-widget-code-highlight\" data-id=\"a718abd\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>\r\n\r\nkaryotype = Sind_karyotype.txt #\u6307\u5b9a\u67d3\u8272\u4f53\u6587\u4ef6\r\nchromosomes_units = 1000000  #\u8bbe\u7f6e\u957f\u5ea6\u5355\u4f4d\uff0c\u8868\u793a\u4e3a1M\u957f\u5ea6\u7684\u5e8f\u5217\u4ee3\u8868\u4e3a1u\r\nchromosomes_display_default = yes #\u9ed8\u8ba4\u662f\u5c06\u6240\u6709\u7684\u67d3\u8272\u4f53\u90fd\u5c55\u793a\u51fa\u6765\r\n\r\n##\u8f7d\u5165ideogram\u914d\u7f6e\u548c\u523b\u5ea6\u7ebf\u914d\u7f6e\r\n\r\n<<include ideogram.conf>>\r\nshow_ticks          = yes # \u663e\u793a\u523b\u5ea6\r\nshow_tick_labels    = yes # \u663e\u793a\u523b\u5ea6label\r\n<<include ticks.conf>>\r\n\r\n\r\n##plots block \u7ed8\u5236\u6298\u7ebf\u56fe\u3001\u6563\u70b9\u56fe\u3001\u76f4\u65b9\u56fe\u3001\u70ed\u56fe\u548c\u6587\u672c\u663e\u793a\r\n<plots>\r\n\r\n##\u7ed8\u5236\u76f4\u65b9\u56fe\r\n<plot>\r\ntype = histogram # histogram\u6307\u5b9a\u7ed8\u5236\u76f4\u65b9\u56fe line\u4e3a\u6298\u7ebf\u56fe\uff0cscatter\u4e3a\u6563\u70b9\u56fe\uff0cheatmap\u4e3a\u70ed\u56fe\uff0ctext\u4e3a\u6587\u672c\r\nfile = Sind_genecount.txt #\u6587\u4ef6\u8def\u5f84\r\n# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0\r\nr1 = 0.98r\r\nr0 = 0.92r\r\norientation = out #\u76f4\u65b9\u56fe\u65b9\u5411\uff0cin\u4e3a\u5411\u5185\r\nfill_color = set3-8-qual-1 #\u76f4\u65b9\u56fe\u7684\u586b\u5145\u989c\u8272\r\nthickness = 0p\r\nmax = 10\r\n\r\n# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272\r\n<backgrounds>\r\n<background>\r\ncolor = vvvlgrey\r\n<\/background>\r\n<\/backgrounds>\r\n\r\n<\/plot>\r\n\r\n<plot>\r\ntype = histogram # histogram\u6307\u5b9a\u7ed8\u5236\u76f4\u65b9\u56fe line\u4e3a\u6298\u7ebf\u56fe\uff0cscatter\u4e3a\u6563\u70b9\u56fe>\uff0cheatmap\u4e3a\u70ed\u56fe\uff0ctext\u4e3a\u6587\u672c\r\nfile = Sind_gc.txt #\u6587\u4ef6\u8def\u5f84 \r\n# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0\r\nr1 = 0.90r\r\nr0 = 0.84r\r\norientation = out #\u76f4\u65b9\u56fe\u65b9\u5411\uff0cin\u4e3a\u5411\u5185\r\nfill_color = set3-8-qual-2 #\u76f4\u65b9\u56fe\u7684\u586b\u5145\u989c\u8272\r\nthickness = 0p\r\n\r\n# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272\r\n<backgrounds>\r\n<background>\r\ncolor = vvvlgrey\r\n<\/background>\r\n<\/backgrounds>\r\n\r\n<\/plot>\r\n\r\n<plot>\r\ntype = heatmap # histogram\u6307\u5b9a\u7ed8\u5236\u76f4\u65b9\u56fe line\u4e3a\u6298\u7ebf\u56fe\uff0cscatter\u4e3a\u6563\u70b9\u56fe>\uff0cheatmap\u4e3a\u70ed\u56fe\uff0ctext\u4e3a\u6587\u672c\r\nfile = Sind_repeat_LTR.txt #\u6587\u4ef6\u8def\u5f84 \r\n# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0\r\nr1 = 0.82r\r\nr0 = 0.76r\r\ncolor = oranges-3-seq #\u70ed\u56fe\u7684\u989c\u8272\r\nmax = 0.1\r\n\r\n# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272\r\n<backgrounds>\r\n<background>\r\ncolor = vvvlgrey\r\n<\/background>\r\n<\/backgrounds>\r\n\r\n<\/plot>\r\n\r\n<plot>\r\ntype = heatmap # histogram\u6307\u5b9a\u7ed8\u5236\u76f4\u65b9\u56fe line\u4e3a\u6298\u7ebf\u56fe\uff0cscatter\u4e3a\u6563\u70b9\u56fe>\uff0cheatmap\u4e3a\u70ed\u56fe\uff0ctext\u4e3a\u6587\u672c\r\nfile = Sind_repeat_Gypsy.txt #\u6587\u4ef6\u8def\u5f84 \r\n# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0\r\nr1 = 0.74r\r\nr0 = 0.68r\r\ncolor = blues-3-seq #\u70ed\u56fe\u7684\u989c\u8272\r\nmax = 0.1\r\n\r\n# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272\r\n<backgrounds>\r\n<background>\r\ncolor = vvvlgrey\r\n<\/background>\r\n<\/backgrounds>\r\n\r\n<\/plot>\r\n\r\n<plot>\r\ntype = heatmap # histogram\u6307\u5b9a\u7ed8\u5236\u76f4\u65b9\u56fe line\u4e3a\u6298\u7ebf\u56fe\uff0cscatter\u4e3a\u6563\u70b9\u56fe>\uff0cheatmap\u4e3a\u70ed\u56fe\uff0ctext\u4e3a\u6587\u672c \r\nfile = Sind_repeat_Copia.txt #\u6587\u4ef6\u8def\u5f84\r\n# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0\r\nr1 = 0.66r\r\nr0 = 0.60r\r\ncolor = purples-3-seq #\u70ed\u56fe\u7684\u989c\u8272\r\nmax = 0.1\r\n\r\n# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272\r\n<backgrounds>\r\n<background>\r\ncolor = vvvlgrey\r\n<\/background>\r\n<\/backgrounds>\r\n\r\n<\/plot>\r\n\r\n<plot>\r\ntype = heatmap # histogram\u6307\u5b9a\u7ed8\u5236\u76f4\u65b9\u56fe line\u4e3a\u6298\u7ebf\u56fe\uff0cscatter\u4e3a\u6563\u70b9\u56fe>\uff0cheatmap\u4e3a\u70ed\u56fe\uff0ctext\u4e3a\u6587\u672c \r\nfile = Sind_repeat_DNA.txt #\u6587\u4ef6\u8def\u5f84\r\n# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0\r\nr1 = 0.58r\r\nr0 = 0.52r\r\ncolor = greens-3-seq #\u70ed\u56fe\u7684\u989c\u8272\r\nmax = 0.1\r\n\r\n# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272\r\n<backgrounds>\r\n<background>\r\ncolor = vvvlgrey\r\n<\/background>\r\n<\/backgrounds>\r\n\r\n<\/plot>\r\n\r\n<plot>\r\ntype  = scatter # \u6307\u5b9a\u7ed8\u56fe\u7c7b\u578b\u4e3aline\r\nfile  = gene_expression_sum_in_windows.bed # \u8bbe\u5b9a\u6570\u636e\u6587\u4ef6\u8def\u5f84\r\n# \u8bbe\u5b9a\u56fe\u5f62\u6240\u5904\u4f4d\u7f6e\r\nr1    = 0.50r\r\nr0    = 0.44r\r\nglyph =  circle # circle, rectangle, or triangle\r\nglyph_size = 4p # \u70b9\u5927\u5c0f\r\ncolor = set3-8-qual-8  # \u70b9\u56fe\u7684\u989c\u8272\r\nmax = 100\r\n\r\n<backgrounds>\r\n<background>\r\ncolor = vvvlgrey\r\n<\/background>\r\n<\/backgrounds>\r\n\r\n<\/plot>\r\n\r\n<\/plots>\r\n\r\n##links\u753b\u8fde\u63a5\u7ebf\r\n<links>\r\n\r\n<link>\r\nfile = Sind_links_homologous_only.txt\r\ncolor = set3-8-qual-4  #\u8bbe\u7f6e\u989c\u8272\r\nradius = 0.42r  #\u8bbe\u7f6e link \u66f2\u7ebf\u7684\u534a\u5f84\r\nbezier_radius = 0r #\u8bbe\u7f6e\u8d1d\u585e\u5c14\u66f2\u7ebf\u534a\u5f84\uff0c\u8be5\u503c\u8bbe\u5927\u540e\u66f2\u7ebf\u6241\u5e73\u3002\r\nthickness = 2 #\u8bbe\u7f6e link \u66f2\u7ebf\u7684\u539a\u5ea6\r\n\r\n## ribbon = yes  #\u5c06\u7ebf\u6761\u8fde\u63a5\u6539\u6210\u5e26\u72b6\u8fde\u63a5\r\n\r\n## \u8fd9\u91cc\u6dfb\u52a0\u4e86\u4e00\u4e2a\u51fd\u6570\uff0c\u81ea\u5b9a\u4e49\u6bcf\u4e2a\u540c\u6e90\u67d3\u8272\u4f53\u7ec4\u7684\u67d3\u8272\u4f53\u4e4b\u95f4\u7684\u7684Link\u7ebf\u4e3a\u4e00\u4e2a\u989c\u8272\r\n<rules>\r\n\r\n<rule>\r\n\r\n   condition  = on(Chr01g1) || on(Chr01g2) || on(Chr01g3) || on(Chr01g4) || on(Chr01g5) || on(Chr01g6) || on(Chr01g7) || on(Chr01g8)   \r\n   color = green\r\n\r\n<\/rule>\r\n\r\n<rule>\r\n\r\n   condition  = on(Chr02g1) || on(Chr02g2) || on(Chr02g3) || on(Chr02g4) || on(Chr02g5) || on(Chr02g6) || on(Chr02g7) || on(Chr02g8)\r\n   color = set3-8-qual-1\r\n\r\n<\/rule>\r\n\r\n<\/rule>\r\n\r\n<rule>\r\n\r\n   condition  = on(Chr02g1) || on(Chr02g2) || on(Chr02g3) || on(Chr02g4) || on(Chr02g5) || on(Chr02g6) || on(Chr02g7) || on(Chr02g8)\r\n   color = set3-8-qual-1\r\n\r\n<\/rule>\r\n\r\n<rule>\r\n\r\n   condition  = on(Chr03g1) || on(Chr03g2) || on(Chr03g3) || on(Chr03g4) || on(Chr03g5) || on(Chr03g6) || on(Chr03g7) || on(Chr03g8)\r\n   color = set3-8-qual-2\r\n\r\n<\/rule>\r\n\r\n<rule>\r\n\r\n   condition  = on(Chr04g1) || on(Chr04g2) || on(Chr04g3) || on(Chr04g4) || on(Chr04g5) || on(Chr04g6) || on(Chr04g7) || on(Chr04g8)\r\n   color = set3-8-qual-3\r\n\r\n<\/rule>\r\n\r\n<rule>\r\n\r\n   condition  = on(Chr05g1) || on(Chr05g2) || on(Chr05g3) || on(Chr05g4) || on(Chr05g5) || on(Chr05g6) || on(Chr05g7) || on(Chr05g8)\r\n   color = set3-8-qual-5\r\n\r\n<\/rule>\r\n\r\n<rule>\r\n\r\n   condition  = on(Chr06g1) || on(Chr06g2) || on(Chr06g3) || on(Chr06g4) || on(Chr06g5) || on(Chr06g6) || on(Chr06g7) || on(Chr06g8)\r\n   color = set3-8-qual-6\r\n\r\n<\/rule>\r\n\r\n<rule>\r\n\r\n   condition  = on(Chr07g1) || on(Chr07g2) || on(Chr07g3) || on(Chr07g4) || on(Chr07g5) || on(Chr07g6) || on(Chr07g7) || on(Chr07g8)\r\n   color = set3-8-qual-7\r\n\r\n<\/rule>\r\n\r\n<rule>\r\n\r\n   condition  = on(Chr08g1) || on(Chr08g2) || on(Chr08g3) || on(Chr08g4) || on(Chr08g5) || on(Chr08g6) || on(Chr08g7) || on(Chr08g8)\r\n   color = set3-8-qual-8\r\n\r\n<\/rule>\r\n\r\n\r\n<\/rules>\r\n\r\n<\/link>\r\n\r\n<\/links>\r\n\r\n\r\n##\u4ee5\u4e0b\u90e8\u5206\u901a\u5e38\u4e0d\u505a\u4fee\u6539\r\n#\u8bbe\u7f6e\u56fe\u7247\u53c2\u6570\r\n<image>\r\n<<include etc\/image.conf>>\r\n#\u8986\u76d6\u539f\u6765\u7684\u56fe\u7247\u534a\u5f84\u53c2\u6570\r\n#radius* = 500 \r\n<\/image>\r\n\r\n#\u8bbe\u7f6e\u989c\u8272\uff0c\u5b57\u4f53\uff0c\u586b\u5145\u6a21\u5f0f\u7684\u914d\u7f6e\u4fe1\u606f\uff1a\r\n<<include etc\/colors_fonts_patterns.conf>>\r\n#\u7cfb\u7edf\u4e0edebug\u53c2\u6570\uff1a\r\n<<include etc\/housekeeping.conf>>\r\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6c31fb8 elementor-widget elementor-widget-image\" data-id=\"6c31fb8\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"1024\" height=\"1024\" src=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/circos-1024x1024.png\" class=\"attachment-large size-large wp-image-2139\" alt=\"\" srcset=\"http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/circos-1024x1024.png 1024w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/circos-300x300.png 300w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/circos-150x150.png 150w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/circos-768x768.png 768w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/circos-1536x1536.png 1536w, http:\/\/www.majunpeng.com\/wp-content\/uploads\/2025\/10\/circos-2048x2048.png 2048w\" sizes=\"(max-width: 1024px) 100vw, 1024px\" \/>\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\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>1. \u524d\u8a00 \u57fa\u56e0\u7ec4Circos\u56fe\u57fa\u672c\u4e0a\u662f\u6bcf\u4e2a\u57fa\u56e0\u7ec4\u7814\u7a76\u5fc5\u5907\u7684\uff0c\u4f46\u662f\u4f18\u96c5\u7684\u7ed8\u5236\u4e00\u4e2a\u201c\u4e0d\u666e\u901a\u7684Circos\u56fe\u5462\u201d\uff1f &#8230; <a title=\"\u5982\u4f55\u7ed8\u5236\u4e00\u4e2a\u201d\u4e0d\u666e\u901a\u201c\u7684\u57fa\u56e0\u7ec4Circos\u56fe\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/10\/11\/%e5%a6%82%e4%bd%95%e7%bb%98%e5%88%b6%e4%b8%80%e4%b8%aa%e4%b8%8d%e6%99%ae%e9%80%9a%e7%9a%84%e5%9f%ba%e5%9b%a0%e7%bb%84circos%e5%9b%be\/\" aria-label=\"\u9605\u8bfb \u5982\u4f55\u7ed8\u5236\u4e00\u4e2a\u201d\u4e0d\u666e\u901a\u201c\u7684\u57fa\u56e0\u7ec4Circos\u56fe\">\u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":2139,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-2116","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-6"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ 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