Which genome assembly is used for segment-wise copy number data processing?

Q&A
1

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!

2

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:
gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta

3

Thank you so much for your kindly answer! :slight_smile: