What is I-PV?
Best practices

First Things First...

To be able to use I-PV, you will need 3 things:
1-DOWNLOAD PERL (linux users can skip this; for windows I recommend strawberry perl).
2-DOWNLOAD Circos 0.67-7(If you can't find one in the official website, you download one here).

Make sure you installed circos correctly will all the modules needed. You can easily test this by writing on command line:

>circos -modules

It will list all the modules and their states. For the ones that are not ok, open CPAN client (search for the executable that comes with PERL) and write:

>install whatever:module

Once all modules are installed, extract your I-PV.rar to anywhere. Open the ./script folder and open the 'SNPtoAA' script. Search for 'my $circos' and make sure the path correspond to the correct location of your circos file located in your ./bin folder of circos main directory.

Circos 0.67-7 provides all the features that I-PV needs, even the previous versions down to 0.60 is ok. If you need these versions send me an email, you might not find them on circos official website. However, if you want to use the latest versions, keep in mind that you will need to copy the circos file in the ./bin directory of circos 0.67-7 to the same ./bin directory of the new circos version. This is because the default curred working directory system that circos uses has been changed starting from 0.68 and it requires this quick fix to make it compatible with I-PV. Beware that newer versions of Circos after 0.68 introduces a compulsory white background that will interfere with I-PV's interactive background change feature. What you can do is when you have the html output, open it with a text editor and seach for a group with 'id=bg' and remove it. This should solve your problem.

For the rest follow the tutorials and the videos on the website. Good luck!

Here are some tips for running i-PV and using its output:

i-PV can be run with all versions of circos. Therefore, always check the "$circos" variable to make sure that the script is using the version of circos you want.

Each time you run i-PV, empty the "datatracks", "input" and "output" folders. This will ensure files won't get mixed up during image generation.

You can view the html ouput in any browser. However, you might run into minor bugs in Firefox, Safari, Opera and Explorer. Therefore I recommend Chrome due to robust svg rendering. I am constantly trying optimize and fix issues for other browsers but such optimizations require insertion of obsolete code that makes i-PV harder to maintain later on. Therefore try to use Chrome.

When you are entering your domain regions in the terminal (command line), always enter the regions in order (domain region 20-200 comes before 300-500 etc.). This is not required for the markups.

The html will open at 100% zoom by default. You can change this by holding down ctrl and pressing + or -.

When you take a snapshot do not forget to click on the "Hide Options" button.

Backup the files in the "template" folder before you experiment on them.

While viewing the html output check the console messages time to time by right-clicking on the html and selecting "Inspect element". Go to the console tab and see if you catch any red warnings. If you encounter any, please send a screenshot to ibrahim.tanyalcin@i-pv.org or support@i-pv.org.

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