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--- |
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license: cc-by-4.0 |
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task_categories: |
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- text-generation |
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- token-classification |
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language: |
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- en |
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tags: |
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- genomics |
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- dna |
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- grch38 |
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- human-genome |
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- evo2 |
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- sparse-autoencoder |
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size_categories: |
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- 100K<n<1M |
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--- |
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# Human GRCh38 Genome Segments |
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## Dataset Description |
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This dataset contains 16,384 base pair segments from the human reference genome (GRCh38) prepared for Sparse Autoencoder (SAE) training with the Evo2 model. The segments are extracted using a sliding window approach with 75% overlap. |
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## Dataset Details |
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- **Total segments**: 718,648 |
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- **Segment size**: 16,384 base pairs |
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- **Stride**: 4,096 base pairs (75% overlap) |
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- **Source genome**: GRCh38.primary_assembly (GENCODE Release 41) |
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- **Chromosomes**: chr1-22, chrX, chrY, plus alternative/random contigs |
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- **Filtering**: Segments with >10% N-content removed |
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## Data Structure |
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Each segment contains: |
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- `chromosome`: Chromosome identifier |
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- `start`: Start position (0-based) |
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- `end`: End position (exclusive) |
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- `sequence`: DNA sequence (16,384 bp) |
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- `strand`: Strand orientation (always "+") |
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- `n_content`: Fraction of N bases (ambiguous nucleotides) |
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## Usage |
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```python |
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from datasets import load_dataset |
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# Load the dataset |
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dataset = load_dataset("harari/human_grch38_segment") |
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# Access a segment |
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segment = dataset['train'][0] |
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print(f"Chromosome: {segment['chromosome']}") |
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print(f"Position: {segment['start']}-{segment['end']}") |
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print(f"Sequence length: {len(segment['sequence'])}") |
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``` |
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## Intended Use |
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This dataset is designed for: |
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- Training Sparse Autoencoders on genomic sequences |
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- Analyzing DNA sequence patterns with foundation models |
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- Genomic representation learning |
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- Evo2 model feature extraction and interpretation |
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## Citation |
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If you use this dataset, please cite the original GRCh38 reference genome and GENCODE annotations: |
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``` |
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@article{grch38, |
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title={The reference genome sequence of the human genome}, |
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journal={Nature}, |
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year={2013} |
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} |
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@article{gencode, |
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title={GENCODE: the reference human genome annotation}, |
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journal={Genome Research}, |
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year={2012} |
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} |
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``` |
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## Data Source |
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- Reference genome: GENCODE GRCh38.p13 Release 41 |
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- URL: https://www.gencodegenes.org/human/release_41.html |
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- Processing: Sliding window chunking with N-content filtering |
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## Preprocessing |
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1. Downloaded GRCh38.primary_assembly.genome.fa.gz |
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2. Extracted 16,384 bp segments with 4,096 bp stride |
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3. Filtered segments with >10% N-content |
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4. Added genomic coordinates and metadata |
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## License |
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This dataset is released under CC-BY-4.0 license, consistent with the GENCODE data usage terms. |
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