Comments (7)
Hi!
First of all, thanks so much for using our app. Regarding your question, can you share with me the maf files you have downloaded from TCGA in order to find a solution? I'm not sure what is going on. It could be due to some dependencies changes in newer versions or also to upgrades in the MAF format. We will try to find a quick solution.
Thanks for letting me know!
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Yes Thank you,
That would be very helpful.
Could I have your email to share the files, since they are greater than 10 MB and I am unable to share them on github.
I will just email you a link for my shared dropbox folder
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For dropbox is better to use my gmail: [email protected]. Thanks!
from musica.
Okay thanks I have shared the folder with the files, most of the files are in unzipped format directly from the TCGA and the two unzipped lung cancer MAF files, I was using for analysis
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Hi again, I have tested your MAF files and they worked using the specific R version and dependencies specified in the session info I added to the README in 1111aec. This configuration is the same that is present in our web server. In this case the problem is that our server is currently limited to a maximum of 20 samples.
Hope that helps and thanks for your confidence and feedback!
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from musica.
Hi!
In this case the extractSignatures function of MAFtools allows you to extract a de novo bunch of signatures implicated in the mutational patterns of your samples. However, this approach doesn't allow you to reconstruct your samples using a collection of well-established signatures as it is the case of our MuSiCa application. These are two completely different scenarios. For a more comprehensive explanation you can look at these two recent reviews: Baez-Ortega and Gori, 2019 and Grolleman and Díaz-Gay et al, 2019.
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Related Issues (20)
- Whole Exome Data HOT 4
- Stopped after clicking "Run" button HOT 4
- Error HOT 3
- Mandatory column names HOT 5
- Downloaded plots have cut off info HOT 3
- Problem uploading maf HOT 1
- Problem Installing ShinySky HOT 5
- To be Updated: `bioclite` with `BiocManager` in dependencies check (repo README.md) HOT 1
- Specify R version to be used HOT 2
- Only somatic mutations and SNVs are supposed to be present in the VCF file? HOT 2
- Input is not detected as bcf or vcf format HOT 6
- Could not identify file types except vcfs HOT 2
- musica_env.yml for conda environmet seems to be Mac specific HOT 10
- Web tool error with MAF file HOT 2
- Interspecies usage HOT 1
- Online analysis failed: Disconnected from the server. HOT 3
- Maf file with multiple samples HOT 3
- Run musica with command line HOT 1
- Online version doesnt work HOT 1
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