Open pkglimmer opened 5 years ago
@pkglimmer I'm so sorry, I totally missed your issue :(. I hope you found the scripts useful anyway.
For the analysis we used data as described in the manuscript mentioned in the README file. We also analysed similarily data for pancancer https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(20)30427-8/fulltext with slightly updated script https://github.com/martynaut/pancancer_mirnome
Sorry again.
Hi Martyna,
I am currently doing research on miRNA mutations in lung cancer, and I just found your scripts super useful, but I have a few questions:
How do I get 'Coordinates' and 'Cancer exons' files as the input data? Do they come from TCGA? If so, could you provide an example TCGA link to the file you used?
In the final analysis step (run_mirnaome_analysis.py), what should the input data directory contain? (For example, the dir in your example is '~/dane/HNC/DATA_HNC') If you use .vcf files, could you tell me why not use the aggregated .maf files on TCGA?
In addition, if you can briefly make a list of the various data you used in your lung cancer project, I would be very grateful.
Thanks in advance!!