Hi, as it may seem for my question I'm a newbie at dealing with all the too many databases for sequences.
I have some .maf with mutations of a given cancer, let's say breast cancer, and a given gene, TP53. The .maf clearly says where the mutations start and end. (I'm just interested in point mutations)
The point is that I want to construct a mutated sequence from this mutation data, using the reference sequence a a template, but there are so many different transcripts, so basically I just want to know which one does TCGA uses for references. Is it the whole gen? Or just the exons?
Thanks in advance