{"id":1471,"date":"2025-03-18T16:06:14","date_gmt":"2025-03-18T08:06:14","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1471"},"modified":"2025-03-20T10:10:50","modified_gmt":"2025-03-20T02:10:50","slug":"%e4%bd%bf%e7%94%a8circos%e7%bb%98%e5%88%b6%e5%9b%be%e5%bd%a2%e6%b3%9b%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%9a%84%e5%9c%88%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/03\/18\/%e4%bd%bf%e7%94%a8circos%e7%bb%98%e5%88%b6%e5%9b%be%e5%bd%a2%e6%b3%9b%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%9a%84%e5%9c%88%e5%9b%be\/","title":{"rendered":"\u4f7f\u7528Circos\u7ed8\u5236\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u7684\u5708\u56fe"},"content":{"rendered":"\t\t
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\u4f7f\u7528Circos\u7ed8\u5236\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u7684\u5708\u56fe<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
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1. \u524d\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

\u6700\u8fd1\u521a\u521a\u6784\u5b8c\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\uff0c\u770b\u4e86\u5f88\u591a\u6587\u7ae0\u4e2d\u90fd\u6709\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u7684circos\u56fe\uff0c\u81ea\u5df1\u4e5f\u8bd5\u7740\u6765\u662f\u7528\u6211\u81ea\u5df1\u7684\u6570\u636e\u6765\u590d\u523b\u4e00\u4e2a\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
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2. \u6570\u636e\u51c6\u5907<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

\uff081\uff09\u6bcf\u4e2a\u57fa\u56e0\u7ec4\u4e0e\u53c2\u8003\u57fa\u56e0\u7ec4\u4e4b\u95f4\u7684\u5171\u7ebf\u6027\u6587\u4ef6<\/p>

\uff082\uff09\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4SNP\u7684\u5206\u5e03<\/p>

\uff083\uff09\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u7684\u5927SV\u548c\u5c0fSV\u7684\u5206\u5e03<\/p>

\uff084\uff09circos \u7ed8\u56fe\u9700\u6c42\u7684\u57fa\u7840\u6587\u4ef6<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
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2.1 \u5171\u7ebf\u6027\u5206\u6587\u4ef6<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

\u8fd9\u91cc\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0cCircos\u4e2d\u7ed8\u5236\u57fa\u56e0\u7ec4\u4e4b\u95f4\u5171\u7ebf\u6027\u5e38\u7528\u7684link\u51fd\u6570\uff0c\u5e76\u4e0d\u9002\u5408\u7528\u5728\u56fe\u6cdb\u7684\u5708\u56fe\u91cc\uff0c\u56e0\u4e3a\u4e0d\u80fd\u8bbe\u7f6e\u534a\u5f84\u7684\u8d77\u70b9\u548c\u91cd\u70b9\uff0c\u6240\u4ee5\u8fd9\u91cc\u9009\u62e9\u4ee5\u7a97\u53e3\u7684\u5f62\u5f0f\u7edf\u8ba1\u5171\u7ebf\u6027\u533a\u57df\u7684\u5206\u5e03\uff0c\u6700\u540e\u4f7f\u7528histogram\u51fd\u6570\u8fdb\u884c\u67f1\u72b6\u56fe\u7684\u7ed8\u5236\uff0c\u4ece\u800c\u8fbe\u5230\u76f8\u540c\u7684\u6548\u679c\u3002<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

# \u5171\u7ebf\u6027\u7684\u7ed3\u679c\u9009\u62e9fixchr\u7684\u7edf\u8ba1\u7ed3\u679c<\/p>

awk ‘{print $10, $1, $2, $11, $3, $4}’ Species_alignments.txt|awk ‘$1 == $4’|awk ‘{print $1, $2, $3}’ > Spe
cies_Syn.txt<\/p>

# \u7edf\u8ba1\u6bcf\u4e2a\u7a97\u53e3\u7684\u5171\u7ebf\u6027\u5206\u5e03<\/p>

python3 coverage_window.py -i Species_Syn.txt -o Species_Syn_window.txt -w 50000<\/p>

# \u81f3\u6b64\u7ed3\u675f\uff0cSpecies_Syn_window.txt\u5c31\u662f\u6211\u4eec\u8981\u7ed8\u5236\u5171\u7ebf\u6027\u5206\u5e03\u7684\u67f1\u72b6\u56fe\u6587\u4ef6<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

2.2 & 2.3 \u8ba1\u7b97SNP\u548cSV\u5206\u5e03<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

\u8fd9\u91cc\u7684\u601d\u8def\u5c31\u662f\u4eceCactus-pangenoe\u7684\u7ed3\u679cvcf\u6587\u4ef6\u4e2d\u5206\u79bb\u51fa\u6765SV\u548cSNP\uff0c\u7136\u540e\u8fdb\u884c\u7a97\u53e3\u7684SNP\u6570\u91cf\u7edf\u8ba1\u3002<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

# \u4eceVCF\u6587\u4ef6\u4e2d\u62c6\u5206SNP\u3001large SV\u548csamll SV\uff0c\u8f93\u51fa\u7ed3\u679c\u4f1a\u6709\u4e09\u4e2a\u6587\u4ef6\uff0c\u5206\u522b\u5bf9\u5e94\u4e09\u79cd\u7684VCF<\/p>

python Get_SV_VCF.py -i Chr_1.vcf -o Chr_1<\/p>

# -o \u8f93\u51fa\u7ed3\u679c\u7684\u524d\u7f00<\/p>

# \u7a97\u53e3\u8ba1\u7b97<\/p>

python Get_SV_count_circos.py Combine_SNP.vcf Circos_Combine_SNP.txt
python Get_SV_count_circos.py Combine_SV_large.vcf Circos_Combine_SV_large.txt
python Get_SV_count_circos.py Combine_SV_samll.vcf Circos_Combine_SV_samll.txt<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t

2.4 Circos\u7ed8\u56fe<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

\u4e0d\u8bf4\u5e9f\u8bdd\u76f4\u63a5\u4e0aCiscos\u7684\u7ed8\u56fe\u4ee3\u7801\uff0c\u770b\u4e0d\u61c2\u81ea\u5df1\u53bb\u7f51\u4e0a\u8865\u8bfe\u5427<\/h4>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

karyotype = Genome_karyotype.txt #\u6307\u5b9a\u67d3\u8272\u4f53\u6587\u4ef6
chromosomes_units = 1000000 #\u8bbe\u7f6e\u957f\u5ea6\u5355\u4f4d\uff0c\u8868\u793a\u4e3a1M\u957f\u5ea6\u7684\u5e8f\u5217\u4ee3\u8868\u4e3a1u
chromosomes_display_default = yes #\u9ed8\u8ba4\u662f\u5c06\u6240\u6709\u7684\u67d3\u8272\u4f53\u90fd\u5c55\u793a\u51fa\u6765<\/p>

##\u8f7d\u5165ideogram\u914d\u7f6e\u548c\u523b\u5ea6\u7ebf\u914d\u7f6e<\/p>

<<include ideogram.conf>>
show_ticks = yes # \u663e\u793a\u523b\u5ea6
show_tick_labels = yes # \u663e\u793a\u523b\u5ea6label
<<include ticks.conf>><\/p>


##plots block \u7ed8\u5236\u6298\u7ebf\u56fe\u3001\u6563\u70b9\u56fe\u3001\u76f4\u65b9\u56fe\u3001\u70ed\u56fe\u548c\u6587\u672c\u663e\u793a
<plots><\/p>

##\u7ed8\u5236\u76f4\u65b9\u56fe
<plot>
type = 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
file = Genome_genecount.txt #\u6587\u4ef6\u8def\u5f84
# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0
r1 = 0.98r
r0 = 0.92r
orientation = out #\u76f4\u65b9\u56fe\u65b9\u5411\uff0cin\u4e3a\u5411\u5185
fill_color = set3-8-qual-1 #\u76f4\u65b9\u56fe\u7684\u586b\u5145\u989c\u8272
thickness = 0p
max = 10<\/p>

# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272
<backgrounds>
<background>
color = vvvlgrey
<\/background>
<\/backgrounds><\/p>

<\/plot><\/p>

<plot>
type = 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
file = Genome_gc.txt #\u6587\u4ef6\u8def\u5f84
# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0
r1 = 0.90r
r0 = 0.84r
orientation = out #\u76f4\u65b9\u56fe\u65b9\u5411\uff0cin\u4e3a\u5411\u5185
fill_color = set3-8-qual-2 #\u76f4\u65b9\u56fe\u7684\u586b\u5145\u989c\u8272
thickness = 0p<\/p>

# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272
<backgrounds>
<background>
color = vvvlgrey
<\/background>
<\/backgrounds><\/p>

<\/plot><\/p>

<plot>
type = 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
file = Genome_repeat_LTR.txt #\u6587\u4ef6\u8def\u5f84
# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0
r1 = 0.82r
r0 = 0.76r
orientation = out #\u76f4\u65b9\u56fe\u65b9\u5411\uff0cin\u4e3a\u5411\u5185
fill_color = set3-8-qual-3 #\u76f4\u65b9\u56fe\u7684\u586b\u5145\u989c\u8272
thickness = 0p<\/p>

# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272
<backgrounds>
<background>
color = vvvlgrey
<\/background>
<\/backgrounds><\/p>

<\/plot><\/p>

<plot>
type = 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
file = Genome_repeat_Gypsy.txt #\u6587\u4ef6\u8def\u5f84
# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0
r1 = 0.74r
r0 = 0.68r
orientation = out #\u76f4\u65b9\u56fe\u65b9\u5411\uff0cin\u4e3a\u5411\u5185
fill_color = set3-8-qual-5 #\u76f4\u65b9\u56fe\u7684\u586b\u5145\u989c\u8272
thickness = 0p<\/p>

# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272
<backgrounds>
<background>
color = vvvlgrey
<\/background>
<\/backgrounds><\/p>

<\/plot><\/p>

<plot>
type = 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
file = Genome_repeat_Copia.txt #\u6587\u4ef6\u8def\u5f84
# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0
r1 = 0.66r
r0 = 0.60r
orientation = out #\u76f4\u65b9\u56fe\u65b9\u5411\uff0cin\u4e3a\u5411\u5185
fill_color = set3-8-qual-6 #\u76f4\u65b9\u56fe\u7684\u586b\u5145\u989c\u8272
thickness = 0p<\/p>

# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272
<backgrounds>
<background>
color = vvvlgrey
<\/background>
<\/backgrounds><\/p>

<\/plot><\/p>

<plot>
type = 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
file = Genome_repeat_DNA.txt #\u6587\u4ef6\u8def\u5f84
# \u8bbe\u7f6e\u76f4\u65b9\u56fe\u7684\u4f4d\u7f6e\uff0cr1 > r0
r1 = 0.58r
r0 = 0.52r
orientation = out #\u76f4\u65b9\u56fe\u65b9\u5411\uff0cin\u4e3a\u5411\u5185
fill_color = set3-8-qual-7 #\u76f4\u65b9\u56fe\u7684\u586b\u5145
thickness = 0p<\/p>

# \u8bbe\u5b9a\u76f4\u65b9\u56fe\u7684\u80cc\u666f\u989c\u8272
<backgrounds>
<background>
color = vvvlgrey
<\/background>
<\/backgrounds><\/p>

<\/plot><\/p>

<plot>
type = scatter # \u6307\u5b9a\u7ed8\u56fe\u7c7b\u578b\u4e3aline
file = Genome_RNA_seq.txt # \u8bbe\u5b9a\u6570\u636e\u6587\u4ef6\u8def\u5f84
# \u8bbe\u5b9a\u56fe\u5f62\u6240\u5904\u4f4d\u7f6e
r1 = 0.50r
r0 = 0.44r
glyph = circle # circle, rectangle, or triangle
glyph_size = 4p # \u70b9\u5927\u5c0f
color = set3-8-qual-8 # \u8bbe\u5b9a\u989c\u8272
max = 10000<\/p>

<backgrounds>
<background>
color = vvvlgrey
<\/background>
<\/backgrounds><\/p>

<\/plot><\/p>

<\/plots><\/p>

##links\u753b\u8fde\u63a5\u7ebf
<links><\/p>

<link>
file = Chrysanthemum_rhombifolium_filter_link.txt
color = set3-8-qual-4 #\u8bbe\u7f6e\u989c\u8272
radius = 0.42r #\u8bbe\u7f6e link \u66f2\u7ebf\u7684\u534a\u5f84
bezier_radius = 0r #\u8bbe\u7f6e\u8d1d\u585e\u5c14\u66f2\u7ebf\u534a\u5f84\uff0c\u8be5\u503c\u8bbe\u5927\u540e\u66f2\u7ebf\u6241\u5e73\u3002
thickness = 3 #\u8bbe\u7f6e link \u66f2\u7ebf\u7684\u539a\u5ea6<\/p>

## ribbon = yes #\u5c06\u7ebf\u6761\u8fde\u63a5\u6539\u6210\u5e26\u72b6\u8fde\u63a5
<\/link><\/p>

<\/links><\/p>


##\u4ee5\u4e0b\u90e8\u5206\u901a\u5e38\u4e0d\u505a\u4fee\u6539
#\u8bbe\u7f6e\u56fe\u7247\u53c2\u6570
<image>
<<include etc\/image.conf>>
#\u8986\u76d6\u539f\u6765\u7684\u56fe\u7247\u534a\u5f84\u53c2\u6570
#radius* = 500
<\/image><\/p>

#\u8bbe\u7f6e\u989c\u8272\uff0c\u5b57\u4f53\uff0c\u586b\u5145\u6a21\u5f0f\u7684\u914d\u7f6e\u4fe1\u606f\uff1a
<<include etc\/colors_fonts_patterns.conf>>
#\u7cfb\u7edf\u4e0edebug\u53c2\u6570\uff1a
<<include etc\/housekeeping.conf>><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\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":"

\u4f7f\u7528Circos\u7ed8\u5236\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u7684\u5708\u56fe 1. \u524d\u8a00 \u6700\u8fd1\u521a\u521a\u6784\u5b8c\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\uff0c\u770b\u4e86\u5f88\u591a\u6587\u7ae0\u4e2d\u90fd\u6709\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u7684 … \u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":1481,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-1471","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-6"],"acf":[],"yoast_head":"\n\u4f7f\u7528Circos\u7ed8\u5236\u56fe\u5f62\u6cdb\u57fa\u56e0\u7ec4\u7684\u5708\u56fe - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" 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