Genome Music Modeling Tool

Question

[RoyC]

Does anyone know if I can compare a single genome against a list of other genomes with this program and how would I do it? Currently I can only get it to do an analysis of every combination of genomes in a given group. For example, given genome A, B, and C, I only want to compare A to B and C separately rather than A to B, B to C, A to C.

Thank you!

Answer 1

[Chris Miller]

Can you be more specific about what you're trying to do? MuSiC is designed to take a large number of cancer samples (usually at least a few dozen) and detect patterns of mutations in that cohort. Things like the significantly mutated gene (SMG) test and pathscan are essentially useless without many samples. So no, if you only have three genomes and are trying to compare them to each other, MuSiC is probably not the tool for you.

[RoyC]

The three genomes was just an example. We have many samples and want to run 500 genomes, but only want to compare one genome to the rest of the 499. Thank you!

[Chris Miller]

Okay, the question still stands - what do you mean by "compare"? Until we understand what you're trying to do, it's difficult to answer your question.

For your large cohort, you can certainly identify recurrently mutated genes and pathways, see if any mutations are significantly correlated (or mutually exclusive) and do some basic types of clinical correlation. I suppose you could then see if the same events occur in your single genome.