Raw Read Counts Accession

Hello,

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.

Best Regards,
A. Cenk Aksu
aaksu16@ku.edu.tr

Hi, Are you sure you want Achilles readcounts? These represent the result of CRISPR screens and have no connection to WGS. If a cell line has no Achilles replicates, it has not been screened in Achilles.

LNCAPCLONEFGC is scheduled for future release. 20Q2 readcounts contains all pDNA batches.

Hi,
Thank you for showing my mistake. I want the Achilles read counts, for some comparisons with CRISPR screens we implemented in our lab. So I’m sure that I need the raw counts of achilles.

Is there a file, which presents which cell lines added to the latest release?

I’ve checked again the 20Q2 data and unfortunately I just see three different concentrations (10 ng, 50 ng, 100 ng) from batch 4 (screenshot added). To be sure I’ve downloaded the data again, and file still contain the same pDNAs. Could it be possible to reach to other pDNA batches, especially pDNA batch 3, which is the batch number of our cells lines which we want to compare.

Thanks.

I think the problem is that you are only looking at columns that start with “pDNA”. All columns in the readcounts file should be identified using the file Achilles_replicate_map, never the column name. Columns are pDNA if their DepMap_ID in the Achilles_replicate_map is null. The readcounts include pDNA measurements from batches 2, 3, and 4.

Hello Joshua,

I’ve checked the Achilles_replicate_map and find the pDNA of all batches, which also found in Raw read counts.

Thanks for all the help.