BioCircos2 user manual

2020-02-27 194浏览

  • 1.The online-BioCircos2 A step-by-step guide
  • 2.• Part • Part os2 • Part • Part 1. Get started 2. Customize your own BioCirc 3. Advance 4. Download as a html website
  • 3.• Part 1. Get started
  • 4.Before you start, try a demo first to see what BioCircos2 can do
  • 5.Once you select a demo, such as Demo1, the plot will be displayed at the right side of page. Demo1 display the mutation information in EGFR with domains showing in ARC module.
  • 6.Try to move your mouse over a domain, you can see a interactive reaction with color change and a toolbox showing domain details
  • 7.Try to move your mouse over a mutation, you can also see a interactive reaction with color change and a toolbox showing mutation details
  • 8.You can modify our demo when you select any one of demo or customize your own Biocicos2 here when custom selected.
  • 9.Step1 controls the genome configuration of BioCircos2, we preset some templates here for your convenience or you can customize your own genome with selecting custom.
  • 10.Step2 configures all the modules including Mutation, SNP, CNV, HEATMAP, LINK, SCATTER, ARC, HISTOGRAM, LINE, TEXT and BACKGROUND.
  • 11.Here shows all the added modules so far, here we have already added two modules in Demo1 which is MutationDetails1 and ARC1. You can add a new module with selecting Figure a new module and don’t forget to submit when finishing your module.
  • 12.If you are interested in the detailed configuration of each module, select one and you can see all the parameters and data below. Try to modify and save it to see what changes in plot.
  • 13.If you are not satisfied with the module you add or added in demo, select and remove it!
  • 14.• Part 2. Customize your own BioCirc os2
  • 15.First, select custom if you want to start from scratch
  • 16.Second, select a preset template such as hg19, hg38 or select custom to customize your own genome. Remember to when you configuration. submit finish
  • 17.Select step2 and choose a module here. Here is the example file for chosen module, which you can download to view the data structure.
  • 18.In addition to input text, uploading is also a way to import your own data. If you don’t have propriate data yet, download and try example file! Don’t forget to submit when you finish configuration and the module you submit will displayed in Added modules above.
  • 19.Reminder:The data submitted depends on the current tabPanel you select. Forexample:If you click Submit when you select file load, whatever you input in text input will be ignored
  • 20.• Part 3. Advance
  • 21.You may notice there several advanced options hidden here. Apparently, all advanced parameters are already set if you select a module except custom. For further information, pleasevisit:http://bioinfo.ibp.ac.cn/biocircos/document/biocircos.html#getting-started
  • 22.There are also two hidden advanced options for each modules in step2. Please click DETAILS or Which module should I choose? for brief introduction For further information, pleasevisit:http://bioinfo.ibp.ac.cn/biocircos/document/biocircos.html#getting-started
  • 23.• Part 4. Download as a html website
  • 24.If you finish a plot, congratulation! You can download it to your computer now by clicking this button and add BioCircos2 to your own website.
  • 25.You can find all these files in www/ folder after you decompressing downloaded zip file. You can execute this html directly or copy its source code to your own website.