To make it short, HOW CAN I ANALYZE EXOME-SEQ DATA FROM TCGA PORTAL?
I have downloaded a MAF file (from "Somatic Mutations" (as it reads in the portal) folder), Level 2, from TCGA but the file doesn't quite look like a MAF. It looks pretty much like a spreadsheet when I open in Galaxy, with lots of info, such as Entrez_ID, Centre, NCBI build, Start_position, End_position, Variant_classification, Variant_type, and much more.
I understand that on TCGA, Level 2 data have already been normalized and sometimes curated (as the one I downloaded), but how do I get to extract the mutations from there on an easier way (instead of looking at all the almost 7,000 transcripts mutated individually)?
Is there any tutorial, reference or pipeline you would recommend?
Thanks a lot!