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📊 Available Outputs in AlphaGenome

Complete Output List

AlphaGenome offers 11 different output types for DNA analysis:

🧬 Gene Expression

1. RNA_SEQ

  • Description: Gene expression level prediction via RNA-seq
  • Use: Identify active genes and their expression levels
  • Resolution: Single base

2. CAGE

  • Description: Cap Analysis of Gene Expression
  • Use: Identify transcription start sites (promoters)
  • Resolution: Single base

3. PROCAP

  • Description: Precision Run-On sequencing (PRO-cap)
  • Use: Map transcription start sites with high precision
  • Resolution: Single base

🔬 Chromatin Accessibility

4. ATAC

  • Description: Assay for Transposase-Accessible Chromatin
  • Use: Identify open/accessible chromatin regions
  • Resolution: Single base
  • Application: Find active regulatory elements

5. DNASE

  • Description: DNase I hypersensitivity
  • Use: Identify accessible chromatin regions
  • Resolution: Single base
  • Similar to: ATAC-seq

⚛️ Chromatin Modifications

6. CHIP_HISTONE

  • Description: ChIP-seq for histone markers
  • Includes:
  • H3K27AC - Active enhancers
  • H3K4ME3 - Active promoters
  • H3K27ME3 - Repression (Polycomb)
  • H3K36ME3 - Active gene bodies
  • H3K9ME3 - Heterochromatin
  • And other markers
  • Use: Identify epigenetic state of chromatin
  • Resolution: Single base

7. CHIP_TF

  • Description: ChIP-seq for transcription factors
  • Includes:
  • CTCF - Insulators and loops
  • And other transcription factors
  • Use: Identify TF binding sites
  • Resolution: Single base

🧩 3D Structure and Splicing

8. CONTACT_MAPS

  • Description: Chromatin contact maps (Hi-C like)
  • Use: Predict 3D chromatin interactions
  • Application: Understand nuclear organization

9. SPLICE_JUNCTIONS

  • Description: Splicing junction prediction
  • Use: Identify exons and introns
  • Application: Study alternative splicing

10. SPLICE_SITES

  • Description: Splicing site prediction (5' and 3')
  • Use: Identify splice donor/acceptor sites
  • Resolution: Single base

11. SPLICE_SITE_USAGE

  • Description: Splicing site usage prediction
  • Use: Quantify alternative site usage
  • Application: Study isoforms

💡 Usage Examples

Basic Analysis (Expression and Accessibility)

genomics alphagenome analyze -- \
    -i sequence.fasta \
    -k API_KEY \
    -o results/ \
    --outputs RNA_SEQ CAGE ATAC

Complete Epigenetic Analysis

genomics alphagenome analyze -- \
    -i sequence.fasta \
    -k API_KEY \
    -o results/ \
    --outputs ATAC CHIP_HISTONE CHIP_TF

Splicing Analysis

genomics alphagenome analyze -- \
    -i sequence.fasta \
    -k API_KEY \
    -o results/ \
    --outputs RNA_SEQ SPLICE_JUNCTIONS SPLICE_SITES SPLICE_SITE_USAGE

3D Analysis

genomics alphagenome analyze -- \
    -i sequence.fasta \
    -k API_KEY \
    -o results/ \
    --outputs CONTACT_MAPS CHIP_TF

Complete Analysis

genomics alphagenome analyze -- \
    -i sequence.fasta \
    -k API_KEY \
    -o results/ \
    --outputs RNA_SEQ CAGE ATAC CHIP_HISTONE CHIP_TF DNASE

🔍 How to Check Available Outputs

Run the verification script: 

python scripts/diagnostics/check_alphagenome_outputs.py

This script will list all outputs that your AlphaGenome installation supports.

📋 Comparison with Old Nomenclature

If you've seen documentation with different names, here's the correspondence:

Old Name Correct Name Type
H3K27AC CHIP_HISTONE Histone marker
H3K4ME3 CHIP_HISTONE Histone marker
H3K27ME3 CHIP_HISTONE Histone marker
CTCF CHIP_TF Transcription factor

Note: CHIP_HISTONE and CHIP_TF return predictions for multiple markers/factors, not just one.

🎯 Recommendations by Use Case

1. Regulatory Variant Analysis

--outputs RNA_SEQ CAGE ATAC CHIP_HISTONE
Identifies impact on expression, promoters, and enhancers.

2. Gene Expression Studies

--outputs RNA_SEQ CAGE PROCAP
Characterizes expression and transcription start sites.

3. Regulatory Element Analysis

--outputs ATAC DNASE CHIP_HISTONE CHIP_TF
Identifies enhancers, promoters, and binding sites.

4. Splicing Studies

--outputs RNA_SEQ SPLICE_JUNCTIONS SPLICE_SITES SPLICE_SITE_USAGE
Analyzes splicing patterns and isoforms.

5. 3D Genomics

--outputs CONTACT_MAPS CHIP_TF
Studies nuclear organization and loops.

⚠️ Important Notes

  1. Processing Time: More outputs will take longer to analyze
  2. File Sizes: Some outputs generate large files (especially CONTACT_MAPS)
  3. Resolution: Most offer predictions at single-base resolution
  4. Combinations: You can combine as many outputs as you want

🆘 Troubleshooting

Error: "Output 'X' not available"

Cause: Output doesn't exist or incorrect name
Solution: Run python scripts/diagnostics/check_alphagenome_outputs.py to see correct list

Error: "No valid output specified"

Cause: All requested outputs are invalid
Solution: Use outputs from the list above

Process too slow

Cause: Too many outputs or sequence too long
Solution: Reduce number of outputs or split sequence

For more information: https://www.alphagenomedocs.com/

Last updated: October 2025