We want to compare our WGS data with DepMap, therefore we would like to access the raw read counts to analyze the counts with our own pipeline.
We downloaded the latest (20Q2) and several older (20Q1; 18Q1) Achilles raw read counts. In these raw counts files we are looking for HMEL (ACH-000642), 22Rv1 (ACH-000956), LNCAPCLONEFGC (ACH-000977), DU145 (ACH-000979). We checked sample_info of 20Q2, and achilles_n_replicates are not filled for HMEL, 22Rv1, DU145. For LNCAPCLONEFGC the sample_info presents 2 replicates, whereas we could not find raw read counts. These specific cell lines are also not presented in achilles_replicate_map.
In addition 20Q2 raw read counts only provide batch4 pDNA read counts, and the other batches are not available. But we need to compare the cell lines with specific batches as we checked from achilles_replicate_map file from DepMap.
A. Cenk Aksu