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marcos-diazg / musica

MuSiCa - Mutational Signatures in Cancer
https://www.clinicbarcelona.org/en/idibaps/research-areas/liver-digestive-system-and-metabolism/genetic-predisposition-to-gastrointestinal-cancer/tools
MIT License
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Whole Exome Data #28

Closed fitbio closed 6 years ago

fitbio commented 6 years ago

Can Musica be used for analysis of Whole Exome Data.??

marcos-diazg commented 6 years ago

Yes, you can use MuSiCa app for analysis of WES data. You just have to select this option in the input parameters. Thanks!

fitbio commented 6 years ago

Thank you. I will try it out today. Thank you for your kind reply.

fitbio commented 6 years ago

Thank you. I have used musica for my exome samples. I set the option of whole exome sequencing for my analysis. But regarding the Mutational signatures from my Exome samples, does the trinucleotide frequency of the exomes get normalized to the genome level to compare my signatures with cosmic samples? Because when I set "study" as whole exome or whole genome except Somatic prevalance results, the other results are exactly the same. Does a normalization step of exome to genome actually occur?

marcos-diazg commented 6 years ago

As you commented, MuSiCa just takes the type of analysis input option to correctly calculate the somatic mutational prevalence. Regarding mutational signatures analysis, it makes use of MutationalPatterns package. To my knowledge, it does not perform any kind of normalization. Thank you for your feedback!