2018年11月_whereis redhat

原创 circos - Session 2 - Lesson 2 - Histograms

create data track, draw a histogram, which is a plot-type track. Two kinds of data tracks : plots and links.create an image with one histogram#session/2/2/etc/circos.conf<plots>type ...

2018-11-29 11:56:34 217

原创 circos - Session 2 - Lesson 1 - Ideogram, Tick, Grid and Label Layout

review configuration file for this lesson#shared by all lessons in this session<<include ../etc/karyotype.and.layout.conf>><<include ../etc/ideogram.conf>><<include...

2018-11-28 18:35:46 162

原创 circos -session 1 Lesson 12 Relative and Absolute Ticks

#../../etc/ideogram.conf the following are the default settings. Here for the convenience of comparing the default settings and the new settings with suffix * difference, some unrelated settings ar...

2018-11-28 16:25:01 124

原创 circos-session 1 Lesson 11 Ideogram，Color，Scale，Order and Orientation

data tracksmanipulate what ideogram are displayed, their order and orientationFiltering Ideogramswith a "-" prefix, remove several ideograms from the displaye.g.#./etc/ideogram.confchromos...

2018-11-27 18:18:29 216

原创 circos-session 1 Lesson 10 Drawing Multiple Genomes

karyotypes of actual genomes can be drawn from data available through the UCSC genome browser table viewer.karyotype information about a genome can be obtained by selecting --group-- Mapping and Seq...

2018-11-27 14:48:40 164

原创 circos- Session 1 Lesson 9 Cytogenetic Bands

copyright :Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645the gross structure of chromosomes has been mapped using staining. These ban...

2018-11-27 10:52:19 382

原创 circos-Session 1 Lesson8 Ordering Ideogram Regions

axis breaks helps split an ideogram into two or more pieces. To change the order of these pieces, use --tags--Tags defined by [] and are defined in the chromosomes parameter.chromosome 4 is asso...

2018-11-26 17:10:58 108

原创 circos-Session 1 Lesson 7- Chromosome Breaks

to crop the ideogram of a chromosome to a region, use axis breaks don't want to show part of a chromosome, use a chromosome breakA break is defined analogously to a crop, except that the parameter...

2018-11-23 17:27:03 140

原创 circos- Session 1 Lesson 6 - Drawing Ideogram Regions

Axis Breaksto draw 9-21Mb of chromosome 5 karyotype = ../data/karyotype.5chr.txtchromosomes_units = 1000000chromosomes_display_default = yeschromosomes = chr5=9-21#chromosomes = ...

2018-11-23 16:13:09 142

原创 circos- Session 1 Lesson 5 Ideogram Order

to draw a subset of chromosomes , need to change chromosomes_display_default to no . all of the chromosomes that were defined in the karyotype were shown. this is the default behaviour.to change ...

2018-11-23 15:43:18 127

原创 circos-Session 1 Lession 4 - Ideogram Selection

To draw a subset of chromosomes, you need to change chromosomes_display_default to no.only to show chromosomes chr1, chr2, chr3karyotype = ../data/karyotype.5chr.txtchromosomes_units ...

2018-11-23 13:15:11 256

原创 circos- Session 1 Lesson 3 Changing ideogram scale

scale adjustment is defined in the circos.conf using the chromosomes_scale parameter. The syntax of the value for this parameter is : chromosomes_scale = chr1 = 0,2 , chr2 =2 , chr3 = 10 . which ...

2018-11-22 18:26:16 167

原创 circos- Session 1 Lesson 2 relative ideogram spacing

relative ideogram spacingu , absolute value , relative to the value of chromosomes_unitsr , relative to the total size(size/number of chromosomes) of all displayed ideograms. can keep the sa...

2018-11-22 16:42:49 140

原创 genome visualization with Circos_ session 1 Lesson 1 Drawing and Spacing Ideograms

copyright :Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645thanks to the handsome tools and the creative teams, I have the chance to e...

2018-11-22 11:50:44 202

原创 BGA2017_session1.1

#try to make directory to store the output pictures,but failed, circos regard it and etc/circos.conf as a whole[arthur@localhost 1]$ mkdir exercise_t[arthur@localhost 1]$ lscircos.png circos.svg ...

2018-11-21 17:26:26 276

原创 circos-course-1.1_circos.conf file anotation

#/etc/circos.conf （session1.1文件注释)# karyotype路径指定：上级目录/data/karyotype.5chr.txtkaryotype = ../data/karyotype.5chr.txt#chromosomes_units = 1000000chromosomes_display_default = yes# ...

2018-11-19 18:49:35 132

原创 rpm -ivh install the needed packages for yum

#remove the preinstalled rpm packages[root@localhost Course_material]# rpm -qa|grep yum|xargs rpm -e --nodeps#again list the installed rpm packages [root@localhost Course_material]# rpm -qa|grep #y...

2018-11-19 18:48:54 491

原创 update the dependent rpm packages

[arthur@localhost Desktop]$ pythonPython 2.7.5 (default, Feb 11 2014, 07:46:25) [GCC 4.8.2 20140120 (Red Hat 4.8.2-13)] on linux2Type "help", "copyright", "credits" or "license" for more informati...

2018-11-19 18:48:34 7287

原创 the latest version rpm installation

# 查看python版本[arthur@localhost Desktop]$ pythonPython 2.7.5 (default, Feb 11 2014, 07:46:25) [GCC 4.8.2 20140120 (Red Hat 4.8.2-13)] on linux2Type "help", "copyright", "credits" or "license" for m...

2018-11-19 18:45:50 3136

原创 install CPAN packages

[arthur@localhost Desktop]$ pythonPython 2.7.5 (default, Feb 11 2014, 07:46:25) [GCC 4.8.2 20140120 (Red Hat 4.8.2-13)] on linux2Type "help", "copyright", "credits" or "license" for more informati...

2018-11-19 18:45:29 1985

转载 1th matlab与遗传算法工具箱

matlab：数值计算与可视化。集数值分析，矩阵运算，信号处理和图形显示。遗传算法：genetic algorithm,GA，基础：自然选择和遗传理论，适者生存和染色体随机信息交换机制全局寻优搜索算法，模拟自然生物进化，人工进化方式随即优化搜索。将问题域中的可能解视为个体或染色体，将个体编码成符号串形式，模拟遗传选择和自然淘汰，反复进行遗传学操作。目标适应度函数对每个个体进行评价，辅以全局并行...

2018-11-19 18:45:05 265

原创 try to install CPAN and list installed rpm packages

[arthur@localhost example]$ pwd/home/arthur/BGA2017/Course_material/circos-0.69-6/example[arthur@localhost example]$ cd ../../[arthur@localhost Course_material]$ cd ../[arthur@localhost BGA2017]$...

2018-11-16 18:57:16 1292 1

原创 1.2 check the missed modules,needed for circos

[arthur@localhost Course_material]$ lscircos-0.69-6.tgz June08[arthur@localhost Course_material]$ tar xzf circos-0.69-6.tgz [arthur@localhost Course_material]$ lscircos-0.69-6 circos-0.69-6.tg...

2018-11-16 18:48:15 381

原创 1-1. install circos-0.69-6 on redhat linux server 7

#显示当前路径[arthur@localhost Desktop]$ pwd/home/arthur/Desktop#返回当前用户主目录[arthur@localhost Desktop]$ cd ~[arthur@localhost ~]$ lsDesktop Documents Downloads Music Pictures Public Templates Vi...

2018-11-16 18:36:58 284

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