I'm using GBM data from FireBrowse. I have RNAseq data downloaded from FireBrowse ( file name: GBM.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data) it has total 171 samples.
I want to find the IDH1 mutations in the samples of GBM data. By following this video () i was able to find the samples with IDH1 mutation. Following is the list of those samples: total 14 samples
so according to the sample barcode, thses are the DNA samples. thus to find the RNA samples form the expression set data i matched samples barcode by substituting "D" by "R" for example : TCGA-27-2521-01A-01D-1494-08 -> TCGA-27-2521-01A-01R-1494-08 and i got only 8 samples in the RNAseq data. But i'm not sure if this is correct way to find samples with mutation in the RNAseq data (expression set). (please give suggestion for this process)
1) How to identify the mutation status of samples ?, mutation of interest: IDH1
2) how to find wild type samples for those identified samples.
Thank you all in advance :)