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caravagnalab / revolver

REVOLVER - Repeated Evolution in Cancer
https://caravagnalab.github.io/revolver/
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Input file -- where to obtain the "cluster" input column for the input data. #21

Closed xtmgah closed 5 years ago

xtmgah commented 5 years ago

Hello:

For the input file format, where can I get the cluster information? Which algorithm is better to get the cluster information? is the cluster column are necessary for the input files? Thanks.

caravagn commented 5 years ago

From read counts, you want to run subclonal deconvolution with tools like pyClone, sciCLone etc. Those will return the clustering assignments for you mutations, which are the ones in the cluster column.

If you have a more precise question about the data etc, let me know.

xtmgah commented 5 years ago

Thanks for your replay. Another question for me is should I only included "is.drive=TRUE" mutations or any mutations (including intron and intergenc region) will be used for the phylogenetic tree computing.

caravagn commented 5 years ago

Would you mind describing a bit what kind of study are you trying to do? Type of data, sequencing approach, research hypothesis etc. It is difficult otherwise to give sensitive answers to broad questions like this one; drivers determine the signal to pick up repeated trajectories, but according to the study it might be much more wise to use all mutation data (drivers and non-drivers).

caravagn commented 5 years ago

No reply. I assume this was solved.