Using custom background gene set

[marypiper]

Hi,

I am working with a C. elegans laboratory which performs a large number of RNA-seq experiments. They love your tool, and we appreciate your work to make it user-friendly and to output quality figures. We have been performing some custom analyses where the background is not the whole genome or any of the options that are available on Wormcat. Is it possible to input your own background dataset? I tried looking through the R code and the batch script, but I could not find a way to do this.

Thanks for your help,
Mary

[amykwalker]

Hi Mary,
Amy Walker here...Dan forwarded your email. He's done the code but I manage the questions. If you download the code, you can put your own background in as a new annotation list and then call that when you run the program. We are also testing some additional annotation sublists (for example, for the coding genes that would be useful for proteomics) that we would put on the site in a few months. Would there be any that you would be interested in that you think would be generally useful? Feel free to email me at Amy.walker@umassmed.edu if you need more information. Best, Amy