# Q&A **URL:** https://forum.depmap.org/c/qa/5.md [Latest](https://forum.depmap.org/latest.md) · [Categories](https://forum.depmap.org/categories.md) · [Tags](https://forum.depmap.org/tags.md) --- ## [About the Q&A category](https://forum.depmap.org/t/about-the-q-a-category/16)
**Author:** [@aviad](https://forum.depmap.org/u/aviad)\ **Replies:** 0\ **Last updated:** [June 6, 2020, 3:24pm UTC](https://forum.depmap.org/t/about-the-q-a-category/16 "2020-06-06T15:24:00Z")
Post any questions about the DepMap data, portal, assays, and project here! Please note that we are unable to provide general research and data analysis advice. To create a new post, make sure you are logged in and the… --- ## [Reconstructing WRN broken-(TA)n FPBM with 26Q3 public WGS: systematic ~8.6% scale shift](https://forum.depmap.org/t/reconstructing-wrn-broken-ta-n-fpbm-with-26q3-public-wgs-systematic-8-6-scale-shift/4700)
**Author:** [@f-drakeland](https://forum.depmap.org/u/f-drakeland)\ **Replies:** 0\ **Last updated:** [October 21, 2026, 4:46pm UTC](https://forum.depmap.org/t/reconstructing-wrn-broken-ta-n-fpbm-with-26q3-public-wgs-systematic-8-6-scale-shift/4700 "2026-10-21T16:46:44Z")
Hi all, I’ve been working on a reproducibility project using current DepMap/CCLE public WGS data and wanted to ask about a pattern I found in the reconstruction. I reconstructed the broken-(TA)n repeat phenotype (FPBM)… --- ## [RNA pipeline reference availability ](https://forum.depmap.org/t/rna-pipeline-reference-availability/4646)
**Author:** [@tlee](https://forum.depmap.org/u/tlee)\ **Replies:** 2\ **Last updated:** [October 21, 2026, 7:30am UTC](https://forum.depmap.org/t/rna-pipeline-reference-availability/4646 "2026-10-21T07:30:16Z")
I am trying to run the DepMap Omics RNA pipeline on my own data. The pipeline is available here but the genome reference files in the ‘ccleparams’ bucket are not accessible; specifically I’m getting a 403 Forbidden error… --- ## [Organoid dependency data](https://forum.depmap.org/t/organoid-dependency-data/4671)
**Author:** [@sangkyu.kim](https://forum.depmap.org/u/sangkyu.kim)\ **Replies:** 7\ **Last updated:** [October 14, 2026, 7:01pm UTC](https://forum.depmap.org/t/organoid-dependency-data/4671 "2026-10-14T19:01:23Z")
I tried to find the recently published 3D tumor organoid dependency dataset on the DepMap portal without success. Any guidance would be much appreciated! --- ## [CCLE/Depmap License Clarification](https://forum.depmap.org/t/ccle-depmap-license-clarification/4686)
**Author:** [@sdarabi](https://forum.depmap.org/u/sdarabi)\ **Replies:** 2\ **Last updated:** [October 14, 2026, 11:27am UTC](https://forum.depmap.org/t/ccle-depmap-license-clarification/4686 "2026-10-14T11:27:19Z")
Having trouble finding license terms for the following files, and would appreciate support: harmonized\_MS\_CCLE\_Gygi.csv uniprot\_hugo\_entrez\_id\_mapping.csv OmicsExpressionTPMLogp1HumanProteinCodingGenes.csv Per anothe… --- ## [Regarding Mutation data files in dep map portal](https://forum.depmap.org/t/regarding-mutation-data-files-in-dep-map-portal/4691)
**Author:** [@Debasmita\_Sarma\_Chau](https://forum.depmap.org/u/Debasmita_Sarma_Chau)\ **Replies:** 2\ **Last updated:** [October 14, 2026, 11:25am UTC](https://forum.depmap.org/t/regarding-mutation-data-files-in-dep-map-portal/4691 "2026-10-14T11:25:30Z")
Hi, I have been using CCLE mutation data for some time now. I have a question regarding the mutation data. There is a mutation table on the dep map portal and also there are MAF and csv files for mutation in each release… --- ## [Access to WGS VCF for OCI-LY18 (ACH-001616 / CDS-T3gUBN)](https://forum.depmap.org/t/access-to-wgs-vcf-for-oci-ly18-ach-001616-cds-t3gubn/4697)
**Author:** [@Richard\_Possemato](https://forum.depmap.org/u/Richard_Possemato)\ **Replies:** 3\ **Last updated:** [October 13, 2026, 4:06pm UTC](https://forum.depmap.org/t/access-to-wgs-vcf-for-oci-ly18-ach-001616-cds-t3gubn/4697 "2026-10-13T16:06:54Z")
OmicsProfiles lists WGS profile PR-olxzDg for ACH-001616 (OCI-LY18), sequencing ID CDS-T3gUBN, dated 2024-05-21. However, CDS-T3gUBN is absent from the public depmap-omics-ccle AWS WGS VCF/CRAM inventory and from the CCL… --- ## [Cell line mutation data seems to have changed?](https://forum.depmap.org/t/cell-line-mutation-data-seems-to-have-changed/4441)
**Author:** [@stewarme](https://forum.depmap.org/u/stewarme)\ **Replies:** 5\ **Last updated:** [October 9, 2026, 7:36pm UTC](https://forum.depmap.org/t/cell-line-mutation-data-seems-to-have-changed/4441 "2026-10-09T19:36:43Z")
Hi, I have been looking over cell line mutation data and noticed that some snvs for OCI-AML3 cells are no longer on the list, such as BAX and TP53. Is there a reason for this? Thanks! --- ## [RNAi equivalent of gene dependency probabilities](https://forum.depmap.org/t/rnai-equivalent-of-gene-dependency-probabilities/4682)
**Author:** [@Syed\_Haider](https://forum.depmap.org/u/Syed_Haider)\ **Replies:** 6\ **Last updated:** [October 5, 2026, 9:02pm UTC](https://forum.depmap.org/t/rnai-equivalent-of-gene-dependency-probabilities/4682 "2026-10-05T21:02:56Z")
Hi DepMap team, I notice that for the CRISPR screens, you have the following downloadable dataset: CRISPRGeneDependency.csv: Gene dependency probability estimates for all models in the integrated gene effect. Is there… --- ## [Absolute copy number data release](https://forum.depmap.org/t/absolute-copy-number-data-release/4665)
**Author:** [@liy](https://forum.depmap.org/u/liy)\ **Replies:** 2\ **Last updated:** [September 19, 2026, 1:19pm UTC](https://forum.depmap.org/t/absolute-copy-number-data-release/4665 "2026-09-19T13:19:43Z")
Was OmicsAbsoluteCNGene.csv discontinued after 24Q4? If so, what’s the recommended replacement for absolute copy number data? Thank you! --- ## [Value-free PTEN model projection for DepMap Public 26Q1?](https://forum.depmap.org/t/value-free-pten-model-projection-for-depmap-public-26q1/4672)
**Author:** [@psihshtole](https://forum.depmap.org/u/psihshtole)\ **Replies:** 0\ **Last updated:** [August 20, 2026, 2:00pm UTC](https://forum.depmap.org/t/value-free-pten-model-projection-for-depmap-public-26q1/4672 "2026-08-20T14:00:30Z")
We are assessing whether a public-model study of untreated baseline total PTEN protein is feasible without opening assay matrices. We are not asking for files yet and do not want assay values or participant/donor informa… --- ## [Regarding gene expression and gene effect score](https://forum.depmap.org/t/regarding-gene-expression-and-gene-effect-score/4637)
**Author:** [@SH\_C](https://forum.depmap.org/u/SH_C)\ **Replies:** 2\ **Last updated:** [August 4, 2026, 3:21pm UTC](https://forum.depmap.org/t/regarding-gene-expression-and-gene-effect-score/4637 "2026-08-04T15:21:15Z")
Regarding gene expression and gene effect score, I have found that the mRNA expression of some genes may be unrelated to or inversely proportional to the gene effect score. That is, the greater the dependence of the gene… --- ## [26Q1 OmicsCNGeneWGS.csv normalization](https://forum.depmap.org/t/26q1-omicscngenewgs-csv-normalization/4656)
**Author:** [@bikeuphill](https://forum.depmap.org/u/bikeuphill)\ **Replies:** 1\ **Last updated:** [July 17, 2026, 1:09pm UTC](https://forum.depmap.org/t/26q1-omicscngenewgs-csv-normalization/4656 "2026-07-17T13:09:42Z")
In the 26Q1 OmicsCNGeneWGS.csv release, what is the reported linear copy number ratio normalized against? Does a ratio of ~1.0 incorporate that specific cell line’s own ploidy (e.g. a value of ~1.0 for an unaltered gene … --- ## [How should CRISPRInferredModelEfficacy.csv identifiers be mapped in DepMap Public 26Q1?](https://forum.depmap.org/t/how-should-crisprinferredmodelefficacy-csv-identifiers-be-mapped-in-depmap-public-26q1/4653)
**Author:** [@KonGur](https://forum.depmap.org/u/KonGur)\ **Replies:** 1\ **Last updated:** [July 16, 2026, 3:07pm UTC](https://forum.depmap.org/t/how-should-crisprinferredmodelefficacy-csv-identifiers-be-mapped-in-depmap-public-26q1/4653 "2026-07-16T15:07:27Z")
How should CRISPRInferredModelEfficacy.csv identifiers be mapped in DepMap Public 26Q1? I am working with the DepMap Public 26Q1 files and need to map CRISPRInferredModelEfficacy.csv reproducibly to the screen- and mode… --- ## [Bulk download gene effect z-scores](https://forum.depmap.org/t/bulk-download-gene-effect-z-scores/4649)
**Author:** [@need47](https://forum.depmap.org/u/need47)\ **Replies:** 0\ **Last updated:** [June 30, 2026, 6:14pm UTC](https://forum.depmap.org/t/bulk-download-gene-effect-z-scores/4649 "2026-06-30T18:14:39Z")
To whom it may concern, I want to download the gene effect z-scores for all genes in all cell lines. … Is there a bulk download option available? I don’t see it in the download area. Sincerely Tiejun Cheng NCBI/… --- ## [AUC and Correlation coefficient](https://forum.depmap.org/t/auc-and-correlation-coefficient/4361)
**Author:** [@sudarshs](https://forum.depmap.org/u/sudarshs)\ **Replies:** 2\ **Last updated:** [June 25, 2026, 8:47pm UTC](https://forum.depmap.org/t/auc-and-correlation-coefficient/4361 "2026-06-25T20:47:31Z")
I am new to using Depmap. Just a very simple question. When I enter a drug of interest, it produces a list of genes “Top Correlated Expression”. There are mainly genes with a positive correlation. Just to clarify, do… --- ## [CRISPR co-depency top hits obscured by newly added screens](https://forum.depmap.org/t/crispr-co-depency-top-hits-obscured-by-newly-added-screens/4503)
**Author:** [@phaahr](https://forum.depmap.org/u/phaahr)\ **Replies:** 16\ **Last updated:** [June 25, 2026, 12:34pm UTC](https://forum.depmap.org/t/crispr-co-depency-top-hits-obscured-by-newly-added-screens/4503 "2026-06-25T12:34:04Z")
I find a lot of the CRISPR co-depency top hits that I’ve been looking at for a while have changed in the new update(?). The top gene CRISPR co-dependencies are now often changed and I find that the new genes are from a … --- ## [Help with understanding DepMap Cell line summary](https://forum.depmap.org/t/help-with-understanding-depmap-cell-line-summary/4628)
**Author:** [@wdkruger](https://forum.depmap.org/u/wdkruger)\ **Replies:** 4\ **Last updated:** [June 17, 2026, 5:38pm UTC](https://forum.depmap.org/t/help-with-understanding-depmap-cell-line-summary/4628 "2026-06-17T17:38:16Z")
When I type in a cell line, on the right there is a column Header that says “Molecular Subtypes”. Under this it will often say “Level 0”, and under that it might say “CDKN2A-Lof”. What does Level 0 refer too? Also, ho… --- ## [Aneuploidy score version in DepMap](https://forum.depmap.org/t/aneuploidy-score-version-in-depmap/4625)
**Author:** [@Yeliezer21](https://forum.depmap.org/u/Yeliezer21)\ **Replies:** 1\ **Last updated:** [May 13, 2026, 1:44pm UTC](https://forum.depmap.org/t/aneuploidy-score-version-in-depmap/4625 "2026-05-13T13:44:25Z")
Hi, A year ago Ive done an analysis using the aneuploidy score in the data explorer. Now I wanted to recreate this analysis however the data wasnt there anymore. When looking I found a different version is available f… --- ## [Statistical test used in Custom Analysis (2-class comparison)](https://forum.depmap.org/t/statistical-test-used-in-custom-analysis-2-class-comparison/4622)
**Author:** [@Princy\_Gupta](https://forum.depmap.org/u/Princy_Gupta)\ **Replies:** 0\ **Last updated:** [May 8, 2026, 5:33pm UTC](https://forum.depmap.org/t/statistical-test-used-in-custom-analysis-2-class-comparison/4622 "2026-05-08T17:33:56Z")
I’ve used DepMap’s Custom Analysis 2-class comparison feature to compare three data types between two groups of cell lines : CRISPR Chronos scores Gene expression Metabolite abundance I have two specific ques… --- ## [Duplicate entries](https://forum.depmap.org/t/duplicate-entries/4619)
**Author:** [@bzhang](https://forum.depmap.org/u/bzhang)\ **Replies:** 1\ **Last updated:** [May 4, 2026, 1:18pm UTC](https://forum.depmap.org/t/duplicate-entries/4619 "2026-05-04T13:18:09Z")
I noticed that there are two entries for ACH-003186 in the OmicsExpressionTPMLogp1HumanProteinCodingGenes.csv file, each with different SequencingID and IsDefaultEntryForModel values. Could you clarify why there are dup… --- ## [Celligner median distances](https://forum.depmap.org/t/celligner-median-distances/4618)
**Author:** [@Laura2](https://forum.depmap.org/u/Laura2)\ **Replies:** 0\ **Last updated:** [April 30, 2026, 3:49pm UTC](https://forum.depmap.org/t/celligner-median-distances/4618 "2026-04-30T15:49:12Z")
Hello! I was wondering how the median distance value is calculated in the Celligner “Rank models for selected tumors” page. For example, if I select “Breast” lineage and “All” subtype, is the median distance displayed … --- ## [Replicating 25Q2 / 25Q3 Chronos Gene Effect Scores](https://forum.depmap.org/t/replicating-25q2-25q3-chronos-gene-effect-scores/4540)
**Author:** [@ConorM](https://forum.depmap.org/u/ConorM)\ **Replies:** 2\ **Last updated:** [April 29, 2026, 2:09pm UTC](https://forum.depmap.org/t/replicating-25q2-25q3-chronos-gene-effect-scores/4540 "2026-04-29T14:09:29Z")
I am trying to replicate the 25Q2 Chronos Gene Effect Scores using the Raw CRISPR screen data for the 3 libraries, the 25Q2 readme file describing the step by step Achilles Pipeline and the Chronos GitHub Repository. I h… --- ## [CTRP AUC values interpretation](https://forum.depmap.org/t/ctrp-auc-values-interpretation/4613)
**Author:** [@Wiam\_ABDELATIF](https://forum.depmap.org/u/Wiam_ABDELATIF)\ **Replies:** 0\ **Last updated:** [April 17, 2026, 6:58pm UTC](https://forum.depmap.org/t/ctrp-auc-values-interpretation/4613 "2026-04-17T18:58:08Z")
Hello everyone, This question was already asked here by someone but I wasn’t satisfied with the answer unfortunately… I have downloaded the CTRPv2.0\_2015\_ctd2\_ExpandedDataset file, I want to use the AUC as the measure … --- ## [Missing WGS data for HeLa (ACH-001086) in DepMap / Terra workspace](https://forum.depmap.org/t/missing-wgs-data-for-hela-ach-001086-in-depmap-terra-workspace/4610)
**Author:** [@Jian](https://forum.depmap.org/u/Jian)\ **Replies:** 0\ **Last updated:** [April 12, 2026, 1:30pm UTC](https://forum.depmap.org/t/missing-wgs-data-for-hela-ach-001086-in-depmap-terra-workspace/4610 "2026-04-12T13:30:29Z")
Hi, I am trying to locate the whole-genome sequencing (WGS) data for the HeLa cell line (ACH-001086). However, I was unable to find any corresponding WGS data in: the DepMap Terra workspace (sample/model tables), or … --- ## [Reproducing ScreenGeneEffectUncorrected and CRISPRGeneEffectUncorrected from 25Q3](https://forum.depmap.org/t/reproducing-screengeneeffectuncorrected-and-crisprgeneeffectuncorrected-from-25q3/4572)
**Author:** [@zancoste](https://forum.depmap.org/u/zancoste)\ **Replies:** 2\ **Last updated:** [April 7, 2026, 6:44pm UTC](https://forum.depmap.org/t/reproducing-screengeneeffectuncorrected-and-crisprgeneeffectuncorrected-from-25q3/4572 "2026-04-07T18:44:26Z")
Greeting, I am trying to reproduce the scores listed in ScreenGeneEffectUncorrected.csv and CRISPRGeneEffectUncorrected.csv from the RawReadcounts. I have ran \`chronos\` with 1201 epoches, but my results tend to be sli… --- ## [Aneuploidy score version in DepMap](https://forum.depmap.org/t/aneuploidy-score-version-in-depmap/4603)
**Author:** [@Yeliezer21](https://forum.depmap.org/u/Yeliezer21)\ **Replies:** 1\ **Last updated:** [April 1, 2026, 1:16pm UTC](https://forum.depmap.org/t/aneuploidy-score-version-in-depmap/4603 "2026-04-01T13:16:42Z")
Hi, A year ago Ive done an analysis using the aneuploidy score in the data explorer. Now I wanted to recreate this analysis however the data wasnt there anymore. When looking I found a different version is available f… --- ## [Culture medium question about pyruvate](https://forum.depmap.org/t/culture-medium-question-about-pyruvate/4600)
**Author:** [@Bimo](https://forum.depmap.org/u/Bimo)\ **Replies:** 3\ **Last updated:** [March 31, 2026, 2:36am UTC](https://forum.depmap.org/t/culture-medium-question-about-pyruvate/4600 "2026-03-31T02:36:12Z")
Dear DepMap Portal, I was wondering that if the culture medium is with pyruvate or not, especially the cell line with DMEM. There are mutiple DMEM-high glucose choic from thermo fisher is based on basic DMEM. Our lab pr… --- ## [NF2 damaging mutations](https://forum.depmap.org/t/nf2-damaging-mutations/4596)
**Author:** [@Emilia\_Andrade-Brown](https://forum.depmap.org/u/Emilia_Andrade-Brown)\ **Replies:** 5\ **Last updated:** [March 16, 2026, 8:45pm UTC](https://forum.depmap.org/t/nf2-damaging-mutations/4596 "2026-03-16T20:45:40Z")
Hi, I have been looking into pleural mesothelioma and screening for synthetically lethal targets in NF2-mutant cases. Only two cells lines have been identified as NF2-mutant PM, however a third cell line also contains d… --- ## [MSI annotations](https://forum.depmap.org/t/msi-annotations/644)
**Author:** [@Gabriel\_Simon](https://forum.depmap.org/u/Gabriel_Simon)\ **Replies:** 6\ **Last updated:** [March 16, 2026, 7:06pm UTC](https://forum.depmap.org/t/msi-annotations/644 "2026-03-16T19:06:49Z")
The sample\_info.csv Download shows 18 cell-lines annotated as MSI in the lineage\_molecular\_subtype field. However, the data explorer provides an option to color cell lines by Microsatellite Instability, and provides two… [Next page](https://forum.depmap.org/c/qa/5.md?page=1)