# Issues and Bugs **URL:** https://forum.depmap.org/c/issues/6.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 --- ## [Repurposing Hub Broken Link](https://forum.depmap.org/t/repurposing-hub-broken-link/2950)
**Author:** [@Dario](https://forum.depmap.org/u/Dario)\ **Replies:** 1\ **Last updated:** [December 8, 2023, 9:05pm UTC](https://forum.depmap.org/t/repurposing-hub-broken-link/2950 "2023-12-08T21:05:38Z")
On a compound overview, there is Metadata from the Repurposing Hub which never loads when clicked. --- ## [Home Page Compound Link Broken](https://forum.depmap.org/t/home-page-compound-link-broken/2947)
**Author:** [@Dario](https://forum.depmap.org/u/Dario)\ **Replies:** 3\ **Last updated:** [December 5, 2023, 9:54pm UTC](https://forum.depmap.org/t/home-page-compound-link-broken/2947 "2023-12-05T21:54:38Z")
On the portal’s home page is Dabrafenib compound overview which leads to 404 Not Found. --- ## [Saved PNG is without data points](https://forum.depmap.org/t/saved-png-is-without-data-points/2937)
**Author:** [@Lorenz\_Eing](https://forum.depmap.org/u/Lorenz_Eing)\ **Replies:** 1\ **Last updated:** [November 28, 2023, 8:38pm UTC](https://forum.depmap.org/t/saved-png-is-without-data-points/2937 "2023-11-28T20:38:53Z")
Hi there, I was just trying to save the 2D Landscape and Biomarker plots (DepMap - Broad Institute). The downloaded png file does not show any data points. It would be great getting according plots somehow and if this … --- ## [DNMT3A R635W Mutation in OCIAML2 annotation inconsistency](https://forum.depmap.org/t/dnmt3a-r635w-mutation-in-ociaml2-annotation-inconsistency/2911)
**Author:** [@Yu\_Sun](https://forum.depmap.org/u/Yu_Sun)\ **Replies:** 1\ **Last updated:** [November 8, 2023, 4:57pm UTC](https://forum.depmap.org/t/dnmt3a-r635w-mutation-in-ociaml2-annotation-inconsistency/2911 "2023-11-08T16:57:01Z")
Hi, I noticed annotation inconsistency of the DNMT3A R635W mutation in OCIAML2. If I search for OCIAML2 cell line in the DepMap portal, DNMT3A R635W is annotated as “likely oncogenic” and “likely loss-of-function” in t… --- ## [Unexpected error while doing custom analyses](https://forum.depmap.org/t/unexpected-error-while-doing-custom-analyses/2850)
**Author:** [@rhd10](https://forum.depmap.org/u/rhd10)\ **Replies:** 1\ **Last updated:** [October 24, 2023, 3:29am UTC](https://forum.depmap.org/t/unexpected-error-while-doing-custom-analyses/2850 "2023-10-24T03:29:36Z")
An unexpected error shows up consistently (screenshot attached) when I try to run custom analyses. Kindly help. --- ## [Video tutorials unavailable](https://forum.depmap.org/t/video-tutorials-unavailable/2494)
**Author:** [@JulesL](https://forum.depmap.org/u/JulesL)\ **Replies:** 2\ **Last updated:** [October 16, 2023, 12:55pm UTC](https://forum.depmap.org/t/video-tutorials-unavailable/2494 "2023-10-16T12:55:45Z")
Hello, When trying to open the video tutorial on the Resources pages, I get redirected toward Youtube links but the video are not available anymore (for example : - YouTube) Are these videos available at other links ? … --- ## [Can not load CpG Methylation data](https://forum.depmap.org/t/can-not-load-cpg-methylation-data/2750)
**Author:** [@Nemo](https://forum.depmap.org/u/Nemo)\ **Replies:** 3\ **Last updated:** [August 15, 2023, 9:25am UTC](https://forum.depmap.org/t/can-not-load-cpg-methylation-data/2750 "2023-08-15T09:25:07Z")
Hi, i want to get the information of the CpG Methylation data of gene, when i choose any cancer types, and click “load” button, the page can not display the information, just loading and loading, even waiting for a long… --- ## [Is it correct that only 22/78 SCLC cell lines have essentiality data?](https://forum.depmap.org/t/is-it-correct-that-only-22-78-sclc-cell-lines-have-essentiality-data/2751)
**Author:** [@aaschaffer](https://forum.depmap.org/u/aaschaffer)\ **Replies:** 1\ **Last updated:** [August 14, 2023, 3:36pm UTC](https://forum.depmap.org/t/is-it-correct-that-only-22-78-sclc-cell-lines-have-essentiality-data/2751 "2023-08-14T15:36:45Z")
So far as I can determine there are 78 lines for small cell lung cancer indicated by the string SCLC in column 33 of Cell\_lines\_annotations\_20181226.txt. It seems that only 22/78 of these lines have dependency data in CR… --- ## [OncotreeCode CMLBCRABL1 does not include all cell lines with BCR-ABL fusion](https://forum.depmap.org/t/oncotreecode-cmlbcrabl1-does-not-include-all-cell-lines-with-bcr-abl-fusion/2727)
**Author:** [@bkinedi](https://forum.depmap.org/u/bkinedi)\ **Replies:** 2\ **Last updated:** [August 3, 2023, 10:02am UTC](https://forum.depmap.org/t/oncotreecode-cmlbcrabl1-does-not-include-all-cell-lines-with-bcr-abl-fusion/2727 "2023-08-03T10:02:06Z")
Hi, I’ve been working with lymphoid and myeloid cell lines recently and noticed that the majority of CML cell lines are referenced by their OncotreeCode of CML, whilst a few others are referenced by CMLBCRABL1. I had a … --- ## [Same ModelID with different number of mutation calls between 23Q2 and 22Q4](https://forum.depmap.org/t/same-modelid-with-different-number-of-mutation-calls-between-23q2-and-22q4/2706)
**Author:** [@Alice](https://forum.depmap.org/u/Alice)\ **Replies:** 1\ **Last updated:** [July 31, 2023, 6:44pm UTC](https://forum.depmap.org/t/same-modelid-with-different-number-of-mutation-calls-between-23q2-and-22q4/2706 "2023-07-31T18:44:32Z")
Dear DepMap team, Currently, we are using the DepMap somatic mutations data in one of the our projects, and find for the same ModelID, there are more mutation calls in the OmicsSomaticMutations.csv file of the 23Q2 rele… --- ## [Custom upload "cell line not found error" ](https://forum.depmap.org/t/custom-upload-cell-line-not-found-error/2698)
**Author:** [@Santiago\_Sanchez](https://forum.depmap.org/u/Santiago_Sanchez)\ **Replies:** 1\ **Last updated:** [July 31, 2023, 12:57pm UTC](https://forum.depmap.org/t/custom-upload-cell-line-not-found-error/2698 "2023-07-31T12:57:53Z")
Hello, I am trying to upload custom data using the data explorer. I followed the instructions and uploaded a CSV file with one column with the cell line name and another with the data I am trying to upload. Unfortunatel… --- ## [Problem loading perturbation effect 'explore relationship' pagefor specific genes](https://forum.depmap.org/t/problem-loading-perturbation-effect-explore-relationship-pagefor-specific-genes/2651)
**Author:** [@TslilA](https://forum.depmap.org/u/TslilA)\ **Replies:** 2\ **Last updated:** [July 28, 2023, 2:58pm UTC](https://forum.depmap.org/t/problem-loading-perturbation-effect-explore-relationship-pagefor-specific-genes/2651 "2023-07-28T14:58:27Z")
Hello, I’ve been having problems viewing the ‘explore relationships with other data’ page for specific genes for over a month. I’ll get the page with the “loading” icon, but nothing ever loads: This only happens (re… --- ## [Missing orange (damaging) and red (hot-spot) dots on perturbation plots](https://forum.depmap.org/t/missing-orange-damaging-and-red-hot-spot-dots-on-perturbation-plots/2637)
**Author:** [@Daniel\_Suveges](https://forum.depmap.org/u/Daniel_Suveges)\ **Replies:** 3\ **Last updated:** [July 12, 2023, 8:53am UTC](https://forum.depmap.org/t/missing-orange-damaging-and-red-hot-spot-dots-on-perturbation-plots/2637 "2023-07-12T08:53:31Z")
Hi Guys, Thank you for developing and maintaining this amazing resource! I have a question, which might as well being a bug: I have noticed that on perturbation view on the gene pages, I can’t see cell lines with damagi… --- ## [Entrez Gene ID, a tracked integers ends with ".0" in OmicsSomaticMutations.csv](https://forum.depmap.org/t/entrez-gene-id-a-tracked-integers-ends-with-0-in-omicssomaticmutations-csv/2629)
**Author:** [@Alice](https://forum.depmap.org/u/Alice)\ **Replies:** 1\ **Last updated:** [July 6, 2023, 9:07pm UTC](https://forum.depmap.org/t/entrez-gene-id-a-tracked-integers-ends-with-0-in-omicssomaticmutations-csv/2629 "2023-07-06T21:07:32Z")
EntrezGeneID (Entrez Gene: gene-centered information at NCBI - PMC), is an unique, stable and tracked integers as a gene’s identifier. However the format of this gene stable ID in OmicsSomaticMutations.csv has been chan… --- ## [Duplications of modelIDs???.... 23Q2](https://forum.depmap.org/t/duplications-of-modelids-23q2/2638)
**Author:** [@vineet](https://forum.depmap.org/u/vineet)\ **Replies:** 1\ **Last updated:** [June 20, 2023, 2:41pm UTC](https://forum.depmap.org/t/duplications-of-modelids-23q2/2638 "2023-06-20T14:41:55Z")
Hi! Am I missing to explain myself something here???.. can ModelID be duplicated. from “Omicsprofiles.csv” from 23Q2 ProfileID,ModelConditionID,ModelID,Datatype,WESKit PR-lqUArB,MC-000029-BMZc,ACH-000029,rna,NA PR-p… --- ## [Custom Download](https://forum.depmap.org/t/custom-download/2609)
**Author:** [@klm0510](https://forum.depmap.org/u/klm0510)\ **Replies:** 5\ **Last updated:** [June 14, 2023, 8:47am UTC](https://forum.depmap.org/t/custom-download/2609 "2023-06-14T08:47:56Z")
Hi DepMap, I am trying to download several datasets for 2 genes via the custom download, but the download button is greyed out/non responsive. Is there a problem with the system or just me having this problem? Thanks f… --- ## [Missing CRISPRGeneEffect values in 23Q2 release](https://forum.depmap.org/t/missing-crisprgeneeffect-values-in-23q2-release/2604)
**Author:** [@BastiaanSpanjaard](https://forum.depmap.org/u/BastiaanSpanjaard)\ **Replies:** 1\ **Last updated:** [June 5, 2023, 3:27pm UTC](https://forum.depmap.org/t/missing-crisprgeneeffect-values-in-23q2-release/2604 "2023-06-05T15:27:07Z")
Hi, There seem to be some missing values in the CRISPRGeneEffect.csv-file in the 23Q2 release, a total of 184,785 by my counting. In contrast, that same file in the 22Q4 release had no missing values. The missing values… --- ## [Are "CCLE Copy Number Variation (CNV) Data" and "CCLE Mutation Data" still available for download?](https://forum.depmap.org/t/are-ccle-copy-number-variation-cnv-data-and-ccle-mutation-data-still-available-for-download/2514)
**Author:** [@lwtan90](https://forum.depmap.org/u/lwtan90)\ **Replies:** 1\ **Last updated:** [June 5, 2023, 1:39pm UTC](https://forum.depmap.org/t/are-ccle-copy-number-variation-cnv-data-and-ccle-mutation-data-still-available-for-download/2514 "2023-06-05T13:39:13Z")
I am unable to find these files for download. I am looking for a csv file with metadata containing total mutations, TMB and CNV burden. --- ## [Cannot download custom proteomics data](https://forum.depmap.org/t/cannot-download-custom-proteomics-data/2440)
**Author:** [@HCH](https://forum.depmap.org/u/HCH)\ **Replies:** 3\ **Last updated:** [May 31, 2023, 2:27pm UTC](https://forum.depmap.org/t/cannot-download-custom-proteomics-data/2440 "2023-05-31T14:27:08Z")
Hello, I was trying to use custom download. When proteomics dataset was selected among others, it would not be included in the downloaded file. If proteomics dataset was the only thing selected, it constantly showed “une… --- ## [22Q4 data, mutation data missing for certain genes](https://forum.depmap.org/t/22q4-data-mutation-data-missing-for-certain-genes/2318)
**Author:** [@AlexBlais](https://forum.depmap.org/u/AlexBlais)\ **Replies:** 2\ **Last updated:** [May 24, 2023, 7:08pm UTC](https://forum.depmap.org/t/22q4-data-mutation-data-missing-for-certain-genes/2318 "2023-05-24T19:08:57Z")
Hello, Looking at the 22Q4 mutational data, I am realizing that some genes known to be mutated in CCLE cell lines are missing any mutation annotation (missing from the “overview” and the “characterization” tabs). An exa… --- ## [The mutations of MTAP don't match with uniprot and ncbi](https://forum.depmap.org/t/the-mutations-of-mtap-dont-match-with-uniprot-and-ncbi/2414)
**Author:** [@Qiang](https://forum.depmap.org/u/Qiang)\ **Replies:** 3\ **Last updated:** [May 1, 2023, 9:28pm UTC](https://forum.depmap.org/t/the-mutations-of-mtap-dont-match-with-uniprot-and-ncbi/2414 "2023-05-01T21:28:52Z")
I found that many of the mutations of MTAP (Uniprot ID: Q13126) don’t match with any sequence from uniprot or ncbi. For example, HCT116 has a mutation p.V106A, but on uniprot, the 106 should be R. And there are many othe… --- ## [LoF annotation in OmicsSomaticMutations.csv](https://forum.depmap.org/t/lof-annotation-in-omicssomaticmutations-csv/2412)
**Author:** [@DOrlando](https://forum.depmap.org/u/DOrlando)\ **Replies:** 1\ **Last updated:** [May 1, 2023, 5:33pm UTC](https://forum.depmap.org/t/lof-annotation-in-omicssomaticmutations-csv/2412 "2023-05-01T17:33:54Z")
In the documentation for the new mutation file, it states that the LoF column should be Y if “loss of function according to revel (score \>.9) or a set of validated BRCA1 locations”. However, only the latter appears to b… --- ## [ACH001956 removed from 22Q4 entirely](https://forum.depmap.org/t/ach001956-removed-from-22q4-entirely/2401)
**Author:** [@klm0510](https://forum.depmap.org/u/klm0510)\ **Replies:** 3\ **Last updated:** [May 1, 2023, 1:47pm UTC](https://forum.depmap.org/t/ach001956-removed-from-22q4-entirely/2401 "2023-05-01T13:47:24Z")
Hi, We have noticed ACH-001956 has been removed from the 22Q4 CCLE entirely. The problem with WGS data for this cell line an others ACH-001955, ACH-001956, ACH-001957 and ACH-000116 have been dropped from the Copy … --- ## [Discrepancies between Hotspot / Damaging mutations (Custom Downloads) and OmicsSomaticMutations.csv (File Downloads)](https://forum.depmap.org/t/discrepancies-between-hotspot-damaging-mutations-custom-downloads-and-omicssomaticmutations-csv-file-downloads/2487)
**Author:** [@Bence\_Szalai](https://forum.depmap.org/u/Bence_Szalai)\ **Replies:** 2\ **Last updated:** [April 25, 2023, 12:52pm UTC](https://forum.depmap.org/t/discrepancies-between-hotspot-damaging-mutations-custom-downloads-and-omicssomaticmutations-csv-file-downloads/2487 "2023-04-25T12:52:57Z")
Hi DepMap team, at first thank you for the great datasets and tools you are providing to the community. I have recently observed a discrepancy between some mutation related files at depmap.org. E.g.: there are severa… --- ## [Retired Ensembl IDs](https://forum.depmap.org/t/retired-ensembl-ids/2442)
**Author:** [@mw222](https://forum.depmap.org/u/mw222)\ **Replies:** 3\ **Last updated:** [April 21, 2023, 8:52pm UTC](https://forum.depmap.org/t/retired-ensembl-ids/2442 "2023-04-21T20:52:40Z")
I use the ensembl IDs for analyzing the expression datasets (specifically the OmicsExpressionGenesExpectedCountProfile.csv) so that I can merge them with my own RNA-seq datasets that were aligned and counts generated usi… --- ## [DepMap Public 22Q4 expectedcount file has cell line ID issue](https://forum.depmap.org/t/depmap-public-22q4-expectedcount-file-has-cell-line-id-issue/2446)
**Author:** [@hsy1470](https://forum.depmap.org/u/hsy1470)\ **Replies:** 1\ **Last updated:** [April 7, 2023, 2:49pm UTC](https://forum.depmap.org/t/depmap-public-22q4-expectedcount-file-has-cell-line-id-issue/2446 "2023-04-07T14:49:55Z")
I downloaded OmicsExpressionGenesExpectedCountProfiles.csv from DepMap release 22Q4. When I opened the file, the cell line ID did not appear properly and a strange ID was displayed. Could you please confirm these issue… --- ## [PANC1005 (ACH-000060) KRAS Mutation Status](https://forum.depmap.org/t/panc1005-ach-000060-kras-mutation-status/2402)
**Author:** [@Yevgeniy\_Gindin](https://forum.depmap.org/u/Yevgeniy_Gindin)\ **Replies:** 1\ **Last updated:** [March 24, 2023, 9:04pm UTC](https://forum.depmap.org/t/panc1005-ach-000060-kras-mutation-status/2402 "2023-03-24T21:04:16Z")
Hello, The PANC1005 line is well characterized as having a KRAS G12D mutation, but this is missing from the latest release of DepMap data while present in the older releases. Is this is indeed the case or have I made a … --- ## [Missing copy number values from the last 5 genes from all the cell lines](https://forum.depmap.org/t/missing-copy-number-values-from-the-last-5-genes-from-all-the-cell-lines/2306)
**Author:** [@Alice](https://forum.depmap.org/u/Alice)\ **Replies:** 1\ **Last updated:** [February 21, 2023, 2:28pm UTC](https://forum.depmap.org/t/missing-copy-number-values-from-the-last-5-genes-from-all-the-cell-lines/2306 "2023-02-21T14:28:30Z")
I am seeing the last 5 genes’ copy number values are missing from all the cell lines with “ProfileType = dna” in the OmicsCNGene.csv of the 22Q4 releasing, downloaded from https://figshare.com/ndownloader/files/38357438 … --- ## [Unable to search anything in the search box](https://forum.depmap.org/t/unable-to-search-anything-in-the-search-box/203)
**Author:** [@jlwu1991](https://forum.depmap.org/u/jlwu1991)\ **Replies:** 7\ **Last updated:** [February 21, 2023, 11:03pm UTC](https://forum.depmap.org/t/unable-to-search-anything-in-the-search-box/203 "2023-02-21T23:03:50Z")
A user report Generally when a gene/compound name typed, the corresponding gene/compound will be listed in the search box. However, recently I was unable to search anything in the search box, anyone could help me out? … --- ## [Different Annotation Transcripts used between cell lines](https://forum.depmap.org/t/different-annotation-transcripts-used-between-cell-lines/1814)
**Author:** [@Jeffrey\_Kooijman](https://forum.depmap.org/u/Jeffrey_Kooijman)\ **Replies:** 2\ **Last updated:** [February 13, 2023, 4:43pm UTC](https://forum.depmap.org/t/different-annotation-transcripts-used-between-cell-lines/1814 "2023-02-13T16:43:29Z")
Hi, For some genes the reported Protein Change is different between cell lines, while the genome change is identical. This is likely caused by mapping of the mutation to different Annotation Transcripts. I suppose the u… [Previous page](https://forum.depmap.org/c/issues/6.md?page=2) [Next page](https://forum.depmap.org/c/issues/6.md?page=4)