Help with MOCCASIN Matrix Set-up

[Matthew Hinderhofer]

Hello,

I am relatively new to bioinformatics and have recently used the MAJIQ workflow. 

I had a question regarding the starting process of using MOCCASIN that I was unable to answer using the documentation in the readme file on Bitbucket. 

I have already used MAJIQ builder to create my .majiq files and would now like to remove the known covariance in my samples (24) to account for batch, sex, cell line, and KO status. 

What would be my next steps in using this package? And could I possibly get some guidance on how I can set up the matrix to account for the covariance of these samples? 

I am more than happy to add further clarifications to help me along in this process.

Thank you,

Matt 

[bsl...@seas.upenn.edu]

Hi Matt, thank you for your question. Please consult the guidance in the Moccasin readme here: https://bitbucket.org/biociphers/moccasin/src/master/ 

This readme attempts to answer the questions you have asked. Please feel free to ask any follow up questions if the guidance is unclear. 

Barry