I’m trying to figure out which reference genome sequence data the fusion gene breakpoints were based on.
I tried to match the HL-60 cell line depmap fusion gene breakpoint data with the WGS data from ncbi at first, but I didn’t know which one to match with.
As of 23Q2, the reference genome used in STAR-Fusion is Hg38. The specific reference files that we input can be found in our public google storage bucket if that’s helpful: gs://ccleparams/references/GRCh38_gencode_v33_CTAT_lib_Apr062020.plug-n-play/ctat_genome_lib_build_dir.
Thank you for your answer.
I tried to access the storage bucket but I don’t have a billing account, so I wasn’t able to. I’m thinking that I could just try with the Hg83 genome reference data from the ncbi. Will there be a problem detecting the exact breakpoints of the fusion gene mensioned in the depmap cell line summary page from the ncbi reference by PCR?