# Feedback & Feature Requests **URL:** https://www.alphagenomecommunity.com/c/feature-requests-feedback/8.md [Latest](https://www.alphagenomecommunity.com/latest.md) · [Categories](https://www.alphagenomecommunity.com/categories.md) · [Tags](https://www.alphagenomecommunity.com/tags.md) --- ## [About the Feedback & Feature Requests category](https://www.alphagenomecommunity.com/t/about-the-feedback-feature-requests-category/19)
**Author:** [@Dhavi](https://www.alphagenomecommunity.com/u/Dhavi)\ **Replies:** 1\ **Last updated:** [March 19, 2026, 11:26pm UTC](https://www.alphagenomecommunity.com/t/about-the-feedback-feature-requests-category/19 "2026-03-19T23:26:44Z")
Suggestions for improving the API and documentation --- ## [Additional search options](https://www.alphagenomecommunity.com/t/additional-search-options/974)
**Author:** [@Guido\_Neidhardt](https://www.alphagenomecommunity.com/u/Guido_Neidhardt)\ **Replies:** 1\ **Last updated:** [September 18, 2026, 2:40pm UTC](https://www.alphagenomecommunity.com/t/additional-search-options/974 "2026-09-18T14:40:55Z")
Hi, thank you for your great work! As many I see AlphaGenome as game changer in genome analysis. I think it would be useful to be able to have more search options in the searchbar similar to those available in the UCSC… --- ## [Offline availability of precomputed scores](https://www.alphagenomecommunity.com/t/offline-availability-of-precomputed-scores/964)
**Author:** [@matthdsm](https://www.alphagenomecommunity.com/u/matthdsm)\ **Replies:** 2\ **Last updated:** [September 10, 2026, 2:51pm UTC](https://www.alphagenomecommunity.com/t/offline-availability-of-precomputed-scores/964 "2026-09-10T14:51:45Z")
Hi, Are there any plans to publish a dataset containing precomputed scores for high throughput (offline) variant annotation through the likes of Ensembl VEP etc. ? This would be a great feature to have and could direct… --- ## [HEK293T (EFO:0001184) DNase-seq and CAGE track availability](https://www.alphagenomecommunity.com/t/hek293t-efo-0001184-dnase-seq-and-cage-track-availability/908)
**Author:** [@marouane53](https://www.alphagenomecommunity.com/u/marouane53)\ **Replies:** 1\ **Last updated:** [May 20, 2026, 8:18pm UTC](https://www.alphagenomecommunity.com/t/hek293t-efo-0001184-dnase-seq-and-cage-track-availability/908 "2026-05-20T20:18:19Z")
Roadmap question: are there plans to extend HEK293T biosample coverage to DNase-seq and CAGE outputs? Currently I see TF ChIP-seq panels for EFO:0001184 but no accessibility tracks. --- ## [NN Architecture](https://www.alphagenomecommunity.com/t/nn-architecture/891)
**Author:** [@Christian\_Frey](https://www.alphagenomecommunity.com/u/Christian_Frey)\ **Replies:** 0\ **Last updated:** [May 11, 2026, 7:25pm UTC](https://www.alphagenomecommunity.com/t/nn-architecture/891 "2026-05-11T19:25:14Z")
I think, given the long-sequence dynamics of DNA, it would be worthwhile to try the SigFormer Architecture (instead of a pure Transformer architecture), combining Mamba and Transformer Architecture and keeping the comput… --- ## [Support for Multi-Base Mutations in AlphaGenome](https://www.alphagenomecommunity.com/t/support-for-multi-base-mutations-in-alphagenome/634)
**Author:** [@Marc\_Amil](https://www.alphagenomecommunity.com/u/Marc_Amil)\ **Replies:** 3\ **Last updated:** [April 29, 2026, 5:19pm UTC](https://www.alphagenomecommunity.com/t/support-for-multi-base-mutations-in-alphagenome/634 "2026-04-29T17:19:39Z")
Hey, I wanted to ask if, instead of introducing single-nucleotide variations and checking their effects on the signal using dna\_model.predict\_variant() — which has been very useful — does AlphaGenome also support mutati… --- ## [Is there a way to obtain embeddings?](https://www.alphagenomecommunity.com/t/is-there-a-way-to-obtain-embeddings/297)
**Author:** [@Xiaohui\_Jiang](https://www.alphagenomecommunity.com/u/Xiaohui_Jiang)\ **Replies:** 3\ **Last updated:** [April 9, 2026, 9:01am UTC](https://www.alphagenomecommunity.com/t/is-there-a-way-to-obtain-embeddings/297 "2026-04-09T09:01:31Z")
Hi, I’m very interested in using AlphaGenome embeddings for downstream analysis. Is there a way to extract embeddings for specific DNA sequences from the api? That would greatly help us in extending the model to specifi… --- ## [Retina tissue - missing from AlphaGenome tissue bank](https://www.alphagenomecommunity.com/t/retina-tissue-missing-from-alphagenome-tissue-bank/801)
**Author:** [@Marianna\_Weener](https://www.alphagenomecommunity.com/u/Marianna_Weener)\ **Replies:** 1\ **Last updated:** [March 20, 2026, 3:26pm UTC](https://www.alphagenomecommunity.com/t/retina-tissue-missing-from-alphagenome-tissue-bank/801 "2026-03-20T15:26:14Z")
How can we add “retina” transcriptome data? Can we upload retina transcriptome and run API to check how it works? Thanks! --- ## [DNA methylation data for gene expression prediction](https://www.alphagenomecommunity.com/t/dna-methylation-data-for-gene-expression-prediction/776)
**Author:** [@Arthur\_Fischbach](https://www.alphagenomecommunity.com/u/Arthur_Fischbach)\ **Replies:** 2\ **Last updated:** [March 2, 2026, 10:22pm UTC](https://www.alphagenomecommunity.com/t/dna-methylation-data-for-gene-expression-prediction/776 "2026-03-02T22:22:42Z")
Hi, thanks for this great model! I wondered whether you plan to train AlphaGenome on DNA methylation data (bisulfite sequencing (WGBS) or methylation array) to predict gene expression? It might be a helpful addition for … --- ## [Typos in "Example analysis workflow: TAL1 locus"](https://www.alphagenomecommunity.com/t/typos-in-example-analysis-workflow-tal1-locus/799)
**Author:** [@HuangruiChu](https://www.alphagenomecommunity.com/u/HuangruiChu)\ **Replies:** 3\ **Last updated:** [February 25, 2026, 9:08am UTC](https://www.alphagenomecommunity.com/t/typos-in-example-analysis-workflow-tal1-locus/799 "2026-02-25T09:08:41Z")
Dear Alphagenome Team: As I was reading the Example analysis workflow: TAL1 locus, I noticed that in the code and comments part, “DNase-seq” is written as “DNAse-seq”. To make it consistent with the format in the paper.… --- ## [Tutorial for Training on New Data?](https://www.alphagenomecommunity.com/t/tutorial-for-training-on-new-data/779)
**Author:** [@Rylie\_Weaver](https://www.alphagenomecommunity.com/u/Rylie_Weaver)\ **Replies:** 1\ **Last updated:** [February 17, 2026, 9:50am UTC](https://www.alphagenomecommunity.com/t/tutorial-for-training-on-new-data/779 "2026-02-17T09:50:39Z")
Hello all! Is there a tutorial for training an AlphaGenome model on new data? I haven’t been able to find one so far. In particular, how to prepare the data/metadata would be very helpful. All the best, Rylie Weaver --- ## [Use alphagenome prediect wheat genome](https://www.alphagenomecommunity.com/t/use-alphagenome-prediect-wheat-genome/177)
**Author:** [@xiexm](https://www.alphagenomecommunity.com/u/xiexm)\ **Replies:** 2\ **Last updated:** [February 5, 2026, 12:49am UTC](https://www.alphagenomecommunity.com/t/use-alphagenome-prediect-wheat-genome/177 "2026-02-05T00:49:54Z")
In my recent exploration of genomic prediction tools, I utilized AlphaGenome, an advanced deep learning framework designed for modeling DNA sequences and predicting functional genomic elements such as RNA-seq profiles… --- ## [Feature request: flexible window width in CenterMaskScorer](https://www.alphagenomecommunity.com/t/feature-request-flexible-window-width-in-centermaskscorer/769)
**Author:** [@Balwierz](https://www.alphagenomecommunity.com/u/Balwierz)\ **Replies:** 0\ **Last updated:** [February 3, 2026, 3:31pm UTC](https://www.alphagenomecommunity.com/t/feature-request-flexible-window-width-in-centermaskscorer/769 "2026-02-03T15:31:54Z")
Right now window widths are predefined, and even the smallest window width is larger than median enhancer width. Supported widths: \[None, 501, 2001, 10001, 100001, 200001\] --- ## [Feature request: custom transcripts in RNA-seq variant scoring](https://www.alphagenomecommunity.com/t/feature-request-custom-transcripts-in-rna-seq-variant-scoring/767)
**Author:** [@Balwierz](https://www.alphagenomecommunity.com/u/Balwierz)\ **Replies:** 0\ **Last updated:** [February 3, 2026, 12:09pm UTC](https://www.alphagenomecommunity.com/t/feature-request-custom-transcripts-in-rna-seq-variant-scoring/767 "2026-02-03T12:09:52Z")
AlphaGenome uses built-in GENCODE v46 gene set for summarising mRNA levels. I would like to extend this to alternative transcript isoforms or custom transcript sets. --- ## [Bananas in ATAC output](https://www.alphagenomecommunity.com/t/bananas-in-atac-output/766)
**Author:** [@Balwierz](https://www.alphagenomecommunity.com/u/Balwierz)\ **Replies:** 0\ **Last updated:** [February 3, 2026, 11:55am UTC](https://www.alphagenomecommunity.com/t/bananas-in-atac-output/766 "2026-02-03T11:55:31Z")
Hi. I predicted ATAC in a 128kib window using each model fold. They are in good concordance, apart from the most important one: ALL\_FOLDS, which shows a bend with respect to all other folds. Is it expected? Is it a bug?… --- ## [101 video feedback](https://www.alphagenomecommunity.com/t/101-video-feedback/749)
**Author:** [@Anjali\_Singh](https://www.alphagenomecommunity.com/u/Anjali_Singh)\ **Replies:** 3\ **Last updated:** [January 30, 2026, 12:02pm UTC](https://www.alphagenomecommunity.com/t/101-video-feedback/749 "2026-01-30T12:02:24Z")
Hi, I went through the 101 video by Google DeepMind. As this video is from Google DeepMind, I was expecting a little detailed explanation of how to use AlphaGenome meaningfully. But unfortunately it was a such a basic vi… --- ## [Suggestion for a new functionality of variant scorer](https://www.alphagenomecommunity.com/t/suggestion-for-a-new-functionality-of-variant-scorer/713)
**Author:** [@Donghyeon\_Baek](https://www.alphagenomecommunity.com/u/Donghyeon_Baek)\ **Replies:** 3\ **Last updated:** [January 27, 2026, 5:47pm UTC](https://www.alphagenomecommunity.com/t/suggestion-for-a-new-functionality-of-variant-scorer/713 "2026-01-27T17:47:49Z")
I want to investigate variant scores for a specific regions of the genomic sequence. Still, the CenterMaskScorer doesn’t support this and only scores around the variant nucleotide (as its name suggests). The problem is t… --- ## [Predict gene-level expression given sequences](https://www.alphagenomecommunity.com/t/predict-gene-level-expression-given-sequences/472)
**Author:** [@pumpkinguagua](https://www.alphagenomecommunity.com/u/pumpkinguagua)\ **Replies:** 4\ **Last updated:** [November 17, 2025, 3:52pm UTC](https://www.alphagenomecommunity.com/t/predict-gene-level-expression-given-sequences/472 "2025-11-17T15:52:47Z")
Hi, Thank you for the great work! I’m interested in how mutated sequences affect gene expression, and I read there is a post showing how to do the RNA expression prediction given a sequence (Uploading sequences to Alpha… --- ## [Coordiate change when predicting long variants](https://www.alphagenomecommunity.com/t/coordiate-change-when-predicting-long-variants/445)
**Author:** [@Jingyu\_Zeng](https://www.alphagenomecommunity.com/u/Jingyu_Zeng)\ **Replies:** 4\ **Last updated:** [November 5, 2025, 7:15pm UTC](https://www.alphagenomecommunity.com/t/coordiate-change-when-predicting-long-variants/445 "2025-11-05T19:15:33Z")
Hi everyone, When I’m doing some longer variants’ expression prediction (long SVs like deletion or insertion), I found that the coordinate of the alternative expression will change with the insertion/deletion, which wil… --- ## [AlphaGenome public URL/ running AG in R](https://www.alphagenomecommunity.com/t/alphagenome-public-url-running-ag-in-r/694)
**Author:** [@Tee\_Dee](https://www.alphagenomecommunity.com/u/Tee_Dee)\ **Replies:** 1\ **Last updated:** [October 18, 2025, 5:16pm UTC](https://www.alphagenomecommunity.com/t/alphagenome-public-url-running-ag-in-r/694 "2025-10-18T17:16:16Z")
Does AlphaGenome have a public URL? I am interested in running AlphaGenome in R, but cannot find the API endpoint to perform the get requests from. Is this information disclosed? Can I run AG in R? --- ## [Versioning for AlphaGenome API and model](https://www.alphagenomecommunity.com/t/versioning-for-alphagenome-api-and-model/676)
**Author:** [@Joe\_Davis](https://www.alphagenomecommunity.com/u/Joe_Davis)\ **Replies:** 2\ **Last updated:** [September 26, 2025, 8:11pm UTC](https://www.alphagenomecommunity.com/t/versioning-for-alphagenome-api-and-model/676 "2025-09-26T20:11:27Z")
Hello, First, thank you for your amazing contributions with this project! My feature request is to offer clearer support for querying specific model and API versions. I have a set of benchmark questions which I frequen… --- ## [Predict\_interval throughput/server-side output averaging](https://www.alphagenomecommunity.com/t/predict-interval-throughput-server-side-output-averaging/639)
**Author:** [@eyes\_r](https://www.alphagenomecommunity.com/u/eyes_r)\ **Replies:** 4\ **Last updated:** [September 5, 2025, 6:18pm UTC](https://www.alphagenomecommunity.com/t/predict-interval-throughput-server-side-output-averaging/639 "2025-09-05T18:18:51Z")
howdy! I was hoping to evaluate AlphaGenome’s full output on an external benchmark, GUANinE. Unfortunately, querying all ~5k output tracks at full 1Mb context size with predict\_interval seems to be rather slow (at 1 infe… --- ## [Interpreting output prediction inconsistency based on the length of input interval](https://www.alphagenomecommunity.com/t/interpreting-output-prediction-inconsistency-based-on-the-length-of-input-interval/619)
**Author:** [@ken\_man](https://www.alphagenomecommunity.com/u/ken_man)\ **Replies:** 1\ **Last updated:** [August 19, 2025, 8:43am UTC](https://www.alphagenomecommunity.com/t/interpreting-output-prediction-inconsistency-based-on-the-length-of-input-interval/619 "2025-08-19T08:43:01Z")
Hi everyone, I am trying to test-run and understand alphagenome prediction with the TG in different tissue context and different sizes of intervals (a gene selectively expressed in the thyroid gland). I have found some … --- ## [Limiting Batch SNP Predictions to Specific Biosamples or Assays to Reduce Runtime and File Size](https://www.alphagenomecommunity.com/t/limiting-batch-snp-predictions-to-specific-biosamples-or-assays-to-reduce-runtime-and-file-size/492)
**Author:** [@Maryam\_Dashtiahangar](https://www.alphagenomecommunity.com/u/Maryam_Dashtiahangar)\ **Replies:** 1\ **Last updated:** [July 23, 2025, 9:33am UTC](https://www.alphagenomecommunity.com/t/limiting-batch-snp-predictions-to-specific-biosamples-or-assays-to-reduce-runtime-and-file-size/492 "2025-07-23T09:33:14Z")
Hello Team, I recently ran a batch prediction on 3,000 autoimmune‑disease–associated SNPs. I know that when predicting individual variants we can specify which assays or biosamples to include, but I was wondering how to… --- ## [Is it possible to add more data for a particular cell type?](https://www.alphagenomecommunity.com/t/is-it-possible-to-add-more-data-for-a-particular-cell-type/141)
**Author:** [@Ilya\_Flyamer](https://www.alphagenomecommunity.com/u/Ilya_Flyamer)\ **Replies:** 4\ **Last updated:** [July 17, 2025, 1:36pm UTC](https://www.alphagenomecommunity.com/t/is-it-possible-to-add-more-data-for-a-particular-cell-type/141 "2025-07-17T13:36:52Z")
Thanks a lot for this great work, and making the model so easy to access! I am working with mouse embryonic stem cells (‘EFO:0004038’). It seems like AlphaGenome can output only contact maps for it… Which to me is very u… --- ## [ISM using REF and ALT sequences as baseline](https://www.alphagenomecommunity.com/t/ism-using-ref-and-alt-sequences-as-baseline/344)
**Author:** [@Marc\_Pielies\_Avelli](https://www.alphagenomecommunity.com/u/Marc_Pielies_Avelli)\ **Replies:** 1\ **Last updated:** [July 11, 2025, 3:34pm UTC](https://www.alphagenomecommunity.com/t/ism-using-ref-and-alt-sequences-as-baseline/344 "2025-07-11T15:34:34Z")
Hi! I’d like to perform ISM using both REF and ALT sequences as the “baseline”. The idea would be to identify the disruption / appearance of new TF motifs or patterns, just like you did in Supplementary Figures 6-8 in t…