I am new to bioinformatics therefore, I apologise I have two basic questions. But I have a MAF file. It is mutational information available for TCGA Pan cancer dataset.
I want to obtain specific cancer types for example, breast cancer examples from this MAF file. I can see that this file has a column with Tumor_Sample_Barcode and Matched_Norm_Sample_Barcode which is of the type TCGA-XX-XXXX-XXX-XXX-XXX-XXXX-XX. Am I supposed to use this barcode to extract examples only for breast cancer? For example 3C in TCGA-3C-AAAU-01A-11D-A41F-09 means that breast cancer as specified here:
If above mentioned technique is fine then I want to download bed file for GC content and histone marks for cell type specific to Breast cancer. How can I do that? I know I should use ENCODE for it but, how can I do it for cell types specific for breast cancer using hg19.
Insights will be appreciated.