# \#omics **URL:** https://forum.depmap.org/tag/omics/4.md [Latest](https://forum.depmap.org/latest.md) · [Categories](https://forum.depmap.org/categories.md) · [Tags](https://forum.depmap.org/tags.md) --- ## [Discrepancy between OmicsAbsoluteCNGene and OmicsAbsoluteCNSegmentsProfile](https://forum.depmap.org/t/discrepancy-between-omicsabsolutecngene-and-omicsabsolutecnsegmentsprofile/4662)
**Author:** [@Connor\_Payne](https://forum.depmap.org/u/Connor_Payne)\ **Replies:** 2\ **Last updated:** [August 3, 2026, 8:24pm UTC](https://forum.depmap.org/t/discrepancy-between-omicsabsolutecngene-and-omicsabsolutecnsegmentsprofile/4662 "2026-08-03T20:24:47Z")
Hi, I was looking at OmicsAbsoluteCNGene values (24Q4) for the gene DCC on chromosome 18q, in relation to the segment value in OmicsAbsoluteCNSegmentsProfile (also 24Q4). For cell line ACH‑000679 (profile ID PR-pjbPYg),… --- ## [TSS\_RRBS\_Methylation\_Data](https://forum.depmap.org/t/tss-rrbs-methylation-data/4659)
**Author:** [@Michele\_Spanu](https://forum.depmap.org/u/Michele_Spanu)\ **Replies:** 0\ **Last updated:** [July 27, 2026, 2:06pm UTC](https://forum.depmap.org/t/tss-rrbs-methylation-data/4659 "2026-07-27T14:06:40Z")
I have noticed that some genes are not available in any of the methylation datasets (CCLE\_RRBS\_TSS\_1kb\_20180614.txt, CCLE\_RRBS\_TSS\_CpG\_clusters\_20180614.txt), but seem to be available through the portal’s Data Explorer. … --- ## [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… --- ## [is CRIPSRGeneEffect X and Y chromosome aware](https://forum.depmap.org/t/is-cripsrgeneeffect-x-and-y-chromosome-aware/4575)
**Author:** [@bommisetti11](https://forum.depmap.org/u/bommisetti11)\ **Replies:** 1\ **Last updated:** [February 12, 2026, 3:02pm UTC](https://forum.depmap.org/t/is-cripsrgeneeffect-x-and-y-chromosome-aware/4575 "2026-02-12T15:02:09Z")
Hello, I am pretty new to using this database, but I was recently trying to analyze CRISPRGeneeffect of certain paralog proteins that are present either on X or Y chromosomes. XX individuals would have two copies of X v… --- ## [Batch correction best practices for DepMap omics expression data 25Q3](https://forum.depmap.org/t/batch-correction-best-practices-for-depmap-omics-expression-data-25q3/4580)
**Author:** [@nehatalluri](https://forum.depmap.org/u/nehatalluri)\ **Replies:** 2\ **Last updated:** [February 5, 2026, 10:11pm UTC](https://forum.depmap.org/t/batch-correction-best-practices-for-depmap-omics-expression-data-25q3/4580 "2026-02-05T22:11:37Z")
I’m using the 25Q3 OmicsExpressionTPMLogp1HumanProteinCodingGenes.csv dataset and had a question about applying batch correction. Currently, it seems like DepMap is looking for an alternative to ComBat to batch correct s… --- ## [Change to fusion calls in 2025 releases?](https://forum.depmap.org/t/change-to-fusion-calls-in-2025-releases/4582)
**Author:** [@will\_ash](https://forum.depmap.org/u/will_ash)\ **Replies:** 1\ **Last updated:** [February 5, 2026, 6:30pm UTC](https://forum.depmap.org/t/change-to-fusion-calls-in-2025-releases/4582 "2026-02-05T18:30:41Z")
Hi, I’m noticing that a fusion in the OMICS Fusions file becomes strongly correlated to sensitivity to KO of a gene I am interested in when I look in the 2025 releases, but not in earlier versions. Please could you let … --- ## [Are sequences for promoter regions available?](https://forum.depmap.org/t/are-sequences-for-promoter-regions-available/4574)
**Author:** [@Smrithi](https://forum.depmap.org/u/Smrithi)\ **Replies:** 2\ **Last updated:** [February 2, 2026, 2:59pm UTC](https://forum.depmap.org/t/are-sequences-for-promoter-regions-available/4574 "2026-02-02T14:59:10Z")
Hi, this is Smrithi here. I would like to know if the promoter sequences of the cell lines are available separately, or need to be obtained from WGS datasets. Thank you. --- ## [Has Chronos2 been adopted in DepMap 25Q3 for gene-effect estimation?](https://forum.depmap.org/t/has-chronos2-been-adopted-in-depmap-25q3-for-gene-effect-estimation/4539)
**Author:** [@Jeffrey25](https://forum.depmap.org/u/Jeffrey25)\ **Replies:** 1\ **Last updated:** [January 6, 2026, 8:59pm UTC](https://forum.depmap.org/t/has-chronos2-been-adopted-in-depmap-25q3-for-gene-effect-estimation/4539 "2026-01-06T20:59:53Z")
Hi DepMap team, I have a question regarding the model used for gene-effect estimation in the most recent releases. I’m aware that Chronos was introduced starting in DepMap 21Q3. Recently, a new version — Chronos2 — wa… --- ## [In 25Q3, mutation annotation vep --distance](https://forum.depmap.org/t/in-25q3-mutation-annotation-vep-distance/4528)
**Author:** [@Alice](https://forum.depmap.org/u/Alice)\ **Replies:** 1\ **Last updated:** [December 8, 2025, 5:46pm UTC](https://forum.depmap.org/t/in-25q3-mutation-annotation-vep-distance/4528 "2025-12-08T17:46:05Z")
Dear DepMap team, In DepMap 25Q3 mutation calling and annotation pipeline, which value(s) is/are used for the vep --distance? It sets the minimum distance (in base pairs) for which upstream / downstream consequences wi… --- ## [Missing Values in the Promoter Methylation File ](https://forum.depmap.org/t/missing-values-in-the-promoter-methylation-file/4484)
**Author:** [@Van](https://forum.depmap.org/u/Van)\ **Replies:** 1\ **Last updated:** [October 27, 2025, 11:04pm UTC](https://forum.depmap.org/t/missing-values-in-the-promoter-methylation-file/4484 "2025-10-27T23:04:55Z")
Hello, I’m currently trying to use methylation file from the “Methylation (1kb upstream TSS)” custom downloads page (downloaded file = Methylation\_(1kb\_upstream\_TSS)\_subsetted\_NAsdropped.csv) to investigate methylation … --- ## [RNA-seq fastq download from 25Q2](https://forum.depmap.org/t/rna-seq-fastq-download-from-25q2/4464)
**Author:** [@Grace](https://forum.depmap.org/u/Grace)\ **Replies:** 1\ **Last updated:** [September 11, 2025, 8:19pm UTC](https://forum.depmap.org/t/rna-seq-fastq-download-from-25q2/4464 "2025-09-11T20:19:06Z")
Hi, it was exciting to see the RNA-seq cell lines has increased to 1600+. I was wondering where i can download the latest RNA-seq fastq files.Thank you! --- ## [Label cell lines based on TP53 mutation](https://forum.depmap.org/t/label-cell-lines-based-on-tp53-mutation/4459)
**Author:** [@Abofazl\_Arab](https://forum.depmap.org/u/Abofazl_Arab)\ **Replies:** 1\ **Last updated:** [September 8, 2025, 2:34pm UTC](https://forum.depmap.org/t/label-cell-lines-based-on-tp53-mutation/4459 "2025-09-08T14:34:19Z")
I’m trying to systematically annotated cell lines based on TP53 mutation status for my research. Looking at the potential “wild type” p53 cell lines (i.e. no p53 mutation report in WGS mutation tables), I noticed HL-60 a… --- ## [Request to include batch information for all datasets](https://forum.depmap.org/t/request-to-include-batch-information-for-all-datasets/4364)
**Author:** [@bkinedi](https://forum.depmap.org/u/bkinedi)\ **Replies:** 2\ **Last updated:** [August 15, 2025, 1:14pm UTC](https://forum.depmap.org/t/request-to-include-batch-information-for-all-datasets/4364 "2025-08-15T13:14:00Z")
I would like to request that you share all of the information you have on batches, such as batch ID, processing date, etc., for all omics datasets. Currently, it is impossible to quantify the extent to which batch effec… --- ## [Model level data for other omics (RPPA, Mass Spec and Methylation data)](https://forum.depmap.org/t/model-level-data-for-other-omics-rppa-mass-spec-and-methylation-data/4397)
**Author:** [@jkreis](https://forum.depmap.org/u/jkreis)\ **Replies:** 1\ **Last updated:** [August 8, 2025, 1:51pm UTC](https://forum.depmap.org/t/model-level-data-for-other-omics-rppa-mass-spec-and-methylation-data/4397 "2025-08-08T13:51:21Z")
Hello, Thanks a lot for this great resource. Currently the OmicsProfiles file only lists rna,wgs and wes data. How do I know which condition was used for other omics? thanks 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 … --- ## [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… --- ## [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 … --- ## [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… --- ## [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 … --- ## [Clarification on Negative Values in Log-Transformed Gene Expression Data](https://forum.depmap.org/t/clarification-on-negative-values-in-log-transformed-gene-expression-data/3902)
**Author:** [@madhu](https://forum.depmap.org/u/madhu)\ **Replies:** 1\ **Last updated:** [January 30, 2025, 10:08pm UTC](https://forum.depmap.org/t/clarification-on-negative-values-in-log-transformed-gene-expression-data/3902 "2025-01-30T22:08:23Z")
I am working with the DepMap expression datasets, and I have a question regarding the log-transformed values in the OmicsExpressionProteinCodingGenesTPMLogp1.csv file. As per the dataset documentation, the expression va… --- ## [OmicsSomaticMutations.csv, multiple mutation rows of the same cell-line and the same gene](https://forum.depmap.org/t/omicssomaticmutations-csv-multiple-mutation-rows-of-the-same-cell-line-and-the-same-gene/3896)
**Author:** [@mw222](https://forum.depmap.org/u/mw222)\ **Replies:** 2\ **Last updated:** [January 10, 2025, 9:16pm UTC](https://forum.depmap.org/t/omicssomaticmutations-csv-multiple-mutation-rows-of-the-same-cell-line-and-the-same-gene/3896 "2025-01-10T21:16:07Z")
Just want to reiterate how thankful I am for all the helpful and quick responses I have had about this dataset. I had a question regarding the OmicsSomaticMutations dataset that is in MAF format. I am a bit naive when i… --- ## [Aneuploidy score](https://forum.depmap.org/t/aneuploidy-score/3883)
**Author:** [@SusanaVM](https://forum.depmap.org/u/SusanaVM)\ **Replies:** 1\ **Last updated:** [January 6, 2025, 10:04pm UTC](https://forum.depmap.org/t/aneuploidy-score/3883 "2025-01-06T22:04:03Z")
Hi all, In the previous Depmap platform there use to be the aneuplidy score dataset. I cannot find it any longer. Could you help me, please? --- ## [Absolute copy number ](https://forum.depmap.org/t/absolute-copy-number/3834)
**Author:** [@beckyliu](https://forum.depmap.org/u/beckyliu)\ **Replies:** 1\ **Last updated:** [December 20, 2024, 2:13pm UTC](https://forum.depmap.org/t/absolute-copy-number/3834 "2024-12-20T14:13:12Z")
The current data version has been upgraded to 24Q2, and there is also Gene-level absolute copy number data (OmicsAbsoluteCNGene.csv). Why is the copy number data displayed on the interface still from the CCLE 2019 versio… --- ## [Copy\_Number\_(Absolute) and OmicsAbsoluteCNGene are Different](https://forum.depmap.org/t/copy-number-absolute-and-omicsabsolutecngene-are-different/3677)
**Author:** [@Mr\_Epimetheus](https://forum.depmap.org/u/Mr_Epimetheus)\ **Replies:** 1\ **Last updated:** [October 24, 2024, 6:09pm UTC](https://forum.depmap.org/t/copy-number-absolute-and-omicsabsolutecngene-are-different/3677 "2024-10-24T18:09:02Z")
Hello, I have noticed that there is a significant difference between the Copy\_Number\_(Absolute) data in the Custom Downloads interface and the OmicsAbsoluteCNGene data in the All Data interface, both in terms of the numb… --- ## [Need File with gene size or FPKM for CCLE RNA expression](https://forum.depmap.org/t/need-file-with-gene-size-or-fpkm-for-ccle-rna-expression/2699)
**Author:** [@mjfreder](https://forum.depmap.org/u/mjfreder)\ **Replies:** 4\ **Last updated:** [September 25, 2024, 5:32pm UTC](https://forum.depmap.org/t/need-file-with-gene-size-or-fpkm-for-ccle-rna-expression/2699 "2024-09-25T17:32:26Z")
I would like to find the CCLE RNA expression file that has either effective gene sizes or FPKM /RPKM (where estimated RSEM values have been used) to do our own normalizations for CCLE gene expression. I don’t like the wa… --- ## [Accessing raw sequencing data](https://forum.depmap.org/t/accessing-raw-sequencing-data/32)
**Author:** [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\ **Replies:** 8\ **Last updated:** [September 8, 2024, 12:55am UTC](https://forum.depmap.org/t/accessing-raw-sequencing-data/32 "2024-09-08T00:55:52Z")
Users have asked us if they can access raw sequencing data (bam/fastq files) of our cell lines. [Next page](https://forum.depmap.org/tag/omics/4.md?match_all_tags=true&page=1&tags%5B%5D=omics)