Copy number alteration prediction from DNA-seq

Question

[ANAM]

I want to do project on copy number alteration prediction from DNA-seq. I have selected cancer type 'Breast cancer'. Dataset requirement is genes, their CNA chromosomal location and DNA sequence ,both for normal and tumor samples. I'm confused where to get CNA sequences for tumor samples and normal sequences.

I really appreciate any help or suggestion!

Answer 1

[Kevin Blighe]

Hello, I presume that you are new to this topic. Therefore, may I suggest that you use TCGAbiolinks and that you follow this workflow? - Example data for TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

For Breast Cancer, the study code is 'TCGA-BRCA'.

Kevin