# Q&A **URL:** https://forum.depmap.org/c/qa/5.md?page=3 [Latest](https://forum.depmap.org/latest.md) · [Categories](https://forum.depmap.org/categories.md) · [Tags](https://forum.depmap.org/tags.md) **Page:** 4 --- ## [DepMap portal cell line mutation,](https://forum.depmap.org/t/depmap-portal-cell-line-mutation/4186)
**Author:** [@dizysky](https://forum.depmap.org/u/dizysky)\ **Replies:** 2\ **Last updated:** [May 5, 2025, 3:00pm UTC](https://forum.depmap.org/t/depmap-portal-cell-line-mutation/4186 "2025-05-05T15:00:33Z")
Hello, What version does the DepMap portal use currently to annotate a mutation in a cancer cell line with the default setting? A couple of cell lines showed a different mutation pattern between cBio (broad 2019 data, … --- ## [Reference genome for mutation data](https://forum.depmap.org/t/reference-genome-for-mutation-data/4176)
**Author:** [@Cecilia\_Matho](https://forum.depmap.org/u/Cecilia_Matho)\ **Replies:** 1\ **Last updated:** [April 30, 2025, 5:12pm UTC](https://forum.depmap.org/t/reference-genome-for-mutation-data/4176 "2025-04-30T17:12:10Z")
Hi, we are looking at the list of mutations for DU145 cell line ( DepMap ID: ACH-000979) and guessing the position is from hg38 genome, can you please confirm this? Thank you very much in advance! --- ## [Batch corrected counts data](https://forum.depmap.org/t/batch-corrected-counts-data/4171)
**Author:** [@wshao](https://forum.depmap.org/u/wshao)\ **Replies:** 2\ **Last updated:** [April 30, 2025, 3:40am UTC](https://forum.depmap.org/t/batch-corrected-counts-data/4171 "2025-04-30T03:40:10Z")
Is there a batch-corrected version of the counts data, that combines the stranded and unstranded RNA-seq profiles? I see there is a batch-corrected form of the log(TPM+1) counts, so I assume the batch-corrected counts we… --- ## [Normalization -TMM](https://forum.depmap.org/t/normalization-tmm/4122)
**Author:** [@AMBREEN](https://forum.depmap.org/u/AMBREEN)\ **Replies:** 3\ **Last updated:** [April 16, 2025, 1:17pm UTC](https://forum.depmap.org/t/normalization-tmm/4122 "2025-04-16T13:17:30Z")
Hi I want to understand that if I have to do TMM normalization rather than using TPM as TPM is not considered a very good parameter to compare across different samples. Which file with Raw reads would be appropriate to … --- ## [Negative goodness of fit](https://forum.depmap.org/t/negative-goodness-of-fit/4124)
**Author:** [@xiewx](https://forum.depmap.org/u/xiewx)\ **Replies:** 0\ **Last updated:** [April 8, 2025, 9:18am UTC](https://forum.depmap.org/t/negative-goodness-of-fit/4124 "2025-04-08T09:18:53Z")
Dear DepMap team, Why some r2 values in the Prism secondary-screen-dose-response-curve-parameters.csv file are negative? Isn’t r2 bounded between 0 and 1? Thanks --- ## [Question about PRISM Drug sensitivity AUC data](https://forum.depmap.org/t/question-about-prism-drug-sensitivity-auc-data/78)
**Author:** [@Jiang\_shaowen](https://forum.depmap.org/u/Jiang_shaowen)\ **Replies:** 7\ **Last updated:** [April 8, 2025, 8:30am UTC](https://forum.depmap.org/t/question-about-prism-drug-sensitivity-auc-data/78 "2025-04-08T08:30:16Z")
Dear DepMap developers, Thanks for developing this amazing tool! I have some questions regarding the data structure, especially for the PRISM drug AUC data. I noticed that some drugs have multiple BROAD IDs, I guess … --- ## [Availability of of RNA-seq bigwig files](https://forum.depmap.org/t/availability-of-of-rna-seq-bigwig-files/4112)
**Author:** [@bernardo-almeida](https://forum.depmap.org/u/bernardo-almeida)\ **Replies:** 2\ **Last updated:** [April 7, 2025, 5:16pm UTC](https://forum.depmap.org/t/availability-of-of-rna-seq-bigwig-files/4112 "2025-04-07T17:16:40Z")
Hello, I am looking for RNA-seq genome-wide coverage data in bigwig format (instead of table with expression per gene). Is this level of data available? Or a level of data that could be converted to bigwig such as bam. T… --- ## [24Q2 - PureCN Integer Copy Number for Chr X and Y](https://forum.depmap.org/t/24q2-purecn-integer-copy-number-for-chr-x-and-y/3575)
**Author:** [@Sanjana\_Srinivasan](https://forum.depmap.org/u/Sanjana_Srinivasan)\ **Replies:** 3\ **Last updated:** [April 6, 2025, 6:21pm UTC](https://forum.depmap.org/t/24q2-purecn-integer-copy-number-for-chr-x-and-y/3575 "2025-04-06T18:21:37Z")
Hello, I am looking through the data release in 24Q2 and notice that the PureCN copy number profiles for both genes and segments do not have data for chromosome X and Y. Is there somewhere I can find this data? Is ther… --- ## [Multiple SMILES in secondary-screen-dose-response-curve-parameters.csv](https://forum.depmap.org/t/multiple-smiles-in-secondary-screen-dose-response-curve-parameters-csv/4111)
**Author:** [@xiewx](https://forum.depmap.org/u/xiewx)\ **Replies:** 0\ **Last updated:** [April 4, 2025, 1:19pm UTC](https://forum.depmap.org/t/multiple-smiles-in-secondary-screen-dose-response-curve-parameters-csv/4111 "2025-04-04T13:19:02Z")
Hello, I hope this message finds you well. I am currently working with the dataset in the file secondary-screen-dose-response-curve-parameters.csv and noticed that the “smiles” column contains multiple SMILES strings se… --- ## [Availability of RNA-seq data after drug treatment](https://forum.depmap.org/t/availability-of-rna-seq-data-after-drug-treatment/4099)
**Author:** [@Giacomo\_Graziano](https://forum.depmap.org/u/Giacomo_Graziano)\ **Replies:** 1\ **Last updated:** [April 1, 2025, 6:22pm UTC](https://forum.depmap.org/t/availability-of-rna-seq-data-after-drug-treatment/4099 "2025-04-01T18:22:30Z")
Hello, I am looking for RNA-seq data of cancer cell lines treated with specific drugs. Could you please provide information on where I can find these datasets within DepMap or if they are available for download? Thank y… --- ## [Mesenchymal models](https://forum.depmap.org/t/mesenchymal-models/4086)
**Author:** [@Mohammad\_Gendy](https://forum.depmap.org/u/Mohammad_Gendy)\ **Replies:** 1\ **Last updated:** [March 24, 2025, 1:34pm UTC](https://forum.depmap.org/t/mesenchymal-models/4086 "2025-03-24T13:34:41Z")
A while ago, I performed a DepMap analysis to find the mean gene effect on Meshenchymal models, as shown in the attached image. Currently, I’m trying to repeat the same query using different parameters, but I can’t fi… --- ## [Cell Line Selection for CRISPR Screen](https://forum.depmap.org/t/cell-line-selection-for-crispr-screen/4087)
**Author:** [@srikarkrishnag](https://forum.depmap.org/u/srikarkrishnag)\ **Replies:** 0\ **Last updated:** [March 23, 2025, 1:17am UTC](https://forum.depmap.org/t/cell-line-selection-for-crispr-screen/4087 "2025-03-23T01:17:52Z")
Hi, This may be a very naive question - apologies in advance. Any help would be much appreciated. I’m trying to design a CRISPR base-editing screen for a list of oncogenes and tumorsupressors. I’m wondering if there is… --- ## [Drug screen data is not availbale or is it chnaged the way we used to access it](https://forum.depmap.org/t/drug-screen-data-is-not-availbale-or-is-it-chnaged-the-way-we-used-to-access-it/4017)
**Author:** [@vaibhavj](https://forum.depmap.org/u/vaibhavj)\ **Replies:** 2\ **Last updated:** [March 20, 2025, 4:16am UTC](https://forum.depmap.org/t/drug-screen-data-is-not-availbale-or-is-it-chnaged-the-way-we-used-to-access-it/4017 "2025-03-20T04:16:24Z")
Dear DepMap members, I am interested in checking the drug sensitivity of melanoma lines to atorvastatin drug and other drugs in relation to the LDLR protein levels. In the past I used to see the options from the drop dow… --- ## [Co-dependency lists?](https://forum.depmap.org/t/co-dependency-lists/4065)
**Author:** [@vasilisgr](https://forum.depmap.org/u/vasilisgr)\ **Replies:** 2\ **Last updated:** [March 14, 2025, 8:08pm UTC](https://forum.depmap.org/t/co-dependency-lists/4065 "2025-03-14T20:08:01Z")
Was wondering if there is a place I can download the full CRISPR co-dependencies (not just top 100), meaning the correlations from DepMap Public 24Q4+Score, Chronos, for all genes? --- ## [Batch corrected Expression Public 24Q4 - What base?](https://forum.depmap.org/t/batch-corrected-expression-public-24q4-what-base/4067)
**Author:** [@bioinformatistOSU](https://forum.depmap.org/u/bioinformatistOSU)\ **Replies:** 1\ **Last updated:** [March 14, 2025, 1:00pm UTC](https://forum.depmap.org/t/batch-corrected-expression-public-24q4-what-base/4067 "2025-03-14T13:00:57Z")
Hey! I am unsure what base the Batch corrected Expression Public 24Q4 expression data comes in. I used the “Create and download a customized dataset” page and selected/downloaded the Batch corrected Expression Public 24Q… --- ## [ list of essential genes for the survival of colorectal cancer cells](https://forum.depmap.org/t/list-of-essential-genes-for-the-survival-of-colorectal-cancer-cells/4068)
**Author:** [@Narsi](https://forum.depmap.org/u/Narsi)\ **Replies:** 0\ **Last updated:** [March 13, 2025, 5:35pm UTC](https://forum.depmap.org/t/list-of-essential-genes-for-the-survival-of-colorectal-cancer-cells/4068 "2025-03-13T17:35:39Z")
I am a data scientist and have recently started working with biological data. I need some guidance: Which version of the dataset should I use to obtain the list of essential genes for the survival of colorectal cancer … --- ## [Row names in the OmicsExpressionTranscripts file](https://forum.depmap.org/t/row-names-in-the-omicsexpressiontranscripts-file/4062)
**Author:** [@SongSong](https://forum.depmap.org/u/SongSong)\ **Replies:** 2\ **Last updated:** [March 13, 2025, 5:34pm UTC](https://forum.depmap.org/t/row-names-in-the-omicsexpressiontranscripts-file/4062 "2025-03-13T17:34:20Z")
Hi, I have a simple question about the OmicsExpressionTranscriptsTPMLogp1Profile file. When I tried to match the row names in it to the model name, I couldn’t find the related information in Model.csv. Is it not fro… --- ## [Annotation version for each release](https://forum.depmap.org/t/annotation-version-for-each-release/4040)
**Author:** [@kent.fung](https://forum.depmap.org/u/kent.fung)\ **Replies:** 4\ **Last updated:** [March 12, 2025, 10:01am UTC](https://forum.depmap.org/t/annotation-version-for-each-release/4040 "2025-03-12T10:01:20Z")
Hi everyone, I have been looking through different GitHub pages and different parts of the website, but I couldn’t locate a page for the annotation used for each release. Is there a page where the GENCODE used for each … --- ## [Drug screening data (PRISM) vs. CRISPR screening data](https://forum.depmap.org/t/drug-screening-data-prism-vs-crispr-screening-data/3980)
**Author:** [@SongSong](https://forum.depmap.org/u/SongSong)\ **Replies:** 3\ **Last updated:** [March 12, 2025, 1:32am UTC](https://forum.depmap.org/t/drug-screening-data-prism-vs-crispr-screening-data/3980 "2025-03-12T01:32:08Z")
Hi, I have a simple question about the results after drug screening and CRISPR screening. TL;DR Can the values in those screenings be considered in the same context? To my knowledge, the CRISPRGeneEffect.csv contains t… --- ## [Is the raw RNAseq available for download from cells released after 2019?](https://forum.depmap.org/t/is-the-raw-rnaseq-available-for-download-from-cells-released-after-2019/3938)
**Author:** [@Rachael](https://forum.depmap.org/u/Rachael)\ **Replies:** 1\ **Last updated:** [March 7, 2025, 4:56pm UTC](https://forum.depmap.org/t/is-the-raw-rnaseq-available-for-download-from-cells-released-after-2019/3938 "2025-03-07T16:56:30Z")
Hello, I am looking for RNAseq data for: NCCIT Tera2 SHSY5Y I see the processed gene counts have been uploaded to the portal, but I cannot find the raw RNAseq files for my own analysis. Previous posts have directed … --- ## [Investigate the expression level of a gene in defined groups](https://forum.depmap.org/t/investigate-the-expression-level-of-a-gene-in-defined-groups/3978)
**Author:** [@Khadija](https://forum.depmap.org/u/Khadija)\ **Replies:** 1\ **Last updated:** [March 7, 2025, 4:38pm UTC](https://forum.depmap.org/t/investigate-the-expression-level-of-a-gene-in-defined-groups/3978 "2025-03-07T16:38:00Z")
I would like to know how to use data explorer to make a plot of Gene A expression between high Gene B expression and low Gene B expression. --- ## [Details of CRISPR experiment: ScreenSequenceMap.csv](https://forum.depmap.org/t/details-of-crispr-experiment-screensequencemap-csv/4021)
**Author:** [@Mr\_Epimetheus](https://forum.depmap.org/u/Mr_Epimetheus)\ **Replies:** 1\ **Last updated:** [March 7, 2025, 4:15pm UTC](https://forum.depmap.org/t/details-of-crispr-experiment-screensequencemap-csv/4021 "2025-03-07T16:15:08Z")
Hello, I would like to know the specific process of conducting CRISPR experiments on DepMap However, I couldn’t find the ScreenSequenceMap.csv mentioned on the webpage. I also tried other search methods but still c… --- ## [WGS MAF file](https://forum.depmap.org/t/wgs-maf-file/4045)
**Author:** [@Preshita\_Dave](https://forum.depmap.org/u/Preshita_Dave)\ **Replies:** 1\ **Last updated:** [March 6, 2025, 4:28pm UTC](https://forum.depmap.org/t/wgs-maf-file/4045 "2025-03-06T16:28:15Z")
Where can I find mutation data for HCC1143 WGS regions? The OmicsSomaticMutations file I downloaded seems to be mostly covering exonic regions and very few intronic regions and I’m actually interested in promoter region … --- ## [Metadata for ssGSEA pathways](https://forum.depmap.org/t/metadata-for-ssgsea-pathways/4028)
**Author:** [@zahragill](https://forum.depmap.org/u/zahragill)\ **Replies:** 3\ **Last updated:** [March 4, 2025, 8:30pm UTC](https://forum.depmap.org/t/metadata-for-ssgsea-pathways/4028 "2025-03-04T20:30:33Z")
Hello all, I am having trouble finding information about the gene set enrichment pathways (columns) in ssGSEA\_Public\_24Q2\_subsetted. For example, I would like to know which genes are included in each pathway or a brief … --- ## [CRISPR KO screens](https://forum.depmap.org/t/crispr-ko-screens/4010)
**Author:** [@idupanloup](https://forum.depmap.org/u/idupanloup)\ **Replies:** 1\ **Last updated:** [February 27, 2025, 5:51pm UTC](https://forum.depmap.org/t/crispr-ko-screens/4010 "2025-02-27T17:51:49Z")
We did our first CRISPR Cas9 KO screen with 2 cancer cell lines of interest in the lab and wanted to compare our results to the ones available at DepMap. I used the MAGeCK-VISPR tool to identify negatively and positivel… --- ## [Mocs3 interacting drugs](https://forum.depmap.org/t/mocs3-interacting-drugs/4012)
**Author:** [@MikeSusaeta](https://forum.depmap.org/u/MikeSusaeta)\ **Replies:** 0\ **Last updated:** [February 26, 2025, 9:14am UTC](https://forum.depmap.org/t/mocs3-interacting-drugs/4012 "2025-02-26T09:14:08Z")
Hello, I am a 3rd year PhD student looking to understand how can I look for the CRISPR libraries and select an existing compound that could inhibit my gene of interest MOCS3. If you could help me out with this, I would v… --- ## [Where can I find the raw genomics sequencing data?](https://forum.depmap.org/t/where-can-i-find-the-raw-genomics-sequencing-data/1353)
**Author:** [@jmmcfarl](https://forum.depmap.org/u/jmmcfarl)\ **Replies:** 15\ **Last updated:** [February 18, 2025, 5:52pm UTC](https://forum.depmap.org/t/where-can-i-find-the-raw-genomics-sequencing-data/1353 "2025-02-18T17:52:30Z")
Many users have asked about how they can access the raw genomics data. While we are still working on a solution for sharing access-controlled data, a large amount of genomics data from over 1000 cell lines that were part… --- ## [Common essential gene list](https://forum.depmap.org/t/common-essential-gene-list/2576)
**Author:** [@Joe\_Dosch](https://forum.depmap.org/u/Joe_Dosch)\ **Replies:** 2\ **Last updated:** [February 8, 2025, 2:28am UTC](https://forum.depmap.org/t/common-essential-gene-list/2576 "2025-02-08T02:28:06Z")
Hello, I’m interested in figuring out how I can download a list of the genes that are scored as “common essential” by the most recent CRISPR (DepMap Public 23Q2+Score, Chronos) data as defined in the portal. Can anyone… --- ## [Phospho-Proteomics data accessibility issue](https://forum.depmap.org/t/phospho-proteomics-data-accessibility-issue/3963)
**Author:** [@cjehanno](https://forum.depmap.org/u/cjehanno)\ **Replies:** 3\ **Last updated:** [February 6, 2025, 7:17pm UTC](https://forum.depmap.org/t/phospho-proteomics-data-accessibility-issue/3963 "2025-02-06T19:17:35Z")
Dear DepMap Team, Couple of weeks ago, I was able to access and download phospho-proteomics data from the DepMap interface, for classical signalling nodes, such as EGFR, AKT, MAPK… etc for which the phospho-status on fe… --- ## [What exactly is the SegmentMean in OmicsCNSegmentsProfile.csv?](https://forum.depmap.org/t/what-exactly-is-the-segmentmean-in-omicscnsegmentsprofile-csv/3947)
**Author:** [@Diego](https://forum.depmap.org/u/Diego)\ **Replies:** 0\ **Last updated:** [February 3, 2025, 2:06pm UTC](https://forum.depmap.org/t/what-exactly-is-the-segmentmean-in-omicscnsegmentsprofile-csv/3947 "2025-02-03T14:06:42Z")
Hi DepMap team, First of all, thank you very much for your great contribution to the scientific community. I am writing here because I have a doubt regarding the OmicsCNSegmentsProfile.csv file. I am interested in the … [Previous page](https://forum.depmap.org/c/qa/5.md?page=2) [Next page](https://forum.depmap.org/c/qa/5.md?page=4)