Hi I was wondering which genome assembly (GRCh38/hg38? If so, exactly what version?) was used as an alignment reference to generate the segment-wise copy number data, i.e., CCLE_segment_cn.csv and CCLE_wes_segment_cn.csv in DepMap Public 21Q4 release. I wanted to design primer sequences to test copy number variations in some cancer cell lines based on the coordinates shown in those data tables. Thank you!
Hi. We use hg38 for the copy number alignment. The reference genome is the Broad hg38 file described here:
Here’s the google cloud storage URI to it:
Thank you so much for your kindly answer!