CNV index

[patelk...@gmail.com]

Hi,

I am unclear on how to set 'cnv_index' when trying to run CODEX2 with negative control regions.

In the vignette, it is mentioned we set it based on prior knowledge or empirically identify common CNV regions by a first-pass CODEX run.

I am trying to do an exploratory analysis on my data, so I don't have any prior knowledge for my exons residing in common CNV regions.

I don't know if I really understand the concept of cnv_index here.

Any help will be appreciated.

Thank you,

Khushbu

[Jiang, Yuchao]

If you don’t have normal control regions or samples, you should use 

https://htmlpreview.github.io/?https://github.com/yuchaojiang/CODEX2/blob/master/demo/CODEX2.html#running-codex2-without-specifying-negative-control-samplesregions

After a first pass run using the above script, you can identify regions with common CNVs and remove such regions to build an index for negative control regions.

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[Sarah D Weisberg]

Hi, I would like to use known regions how would I set the cnv_index if I have the positions (multiple start and ends). 

Thanks for your help. 

SW