---
license: cc-by-4.0
task_categories:
- text-generation
- token-classification
language:
- en
tags:
- genomics
- dna
- grch38
- human-genome
- evo2
- sparse-autoencoder
size_categories:
- 100K<n<1M
---

# Human GRCh38 Genome Segments

## Dataset Description

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.

## Dataset Details

- **Total segments**: 718,648
- **Segment size**: 16,384 base pairs
- **Stride**: 4,096 base pairs (75% overlap)
- **Source genome**: GRCh38.primary_assembly (GENCODE Release 41)
- **Chromosomes**: chr1-22, chrX, chrY, plus alternative/random contigs
- **Filtering**: Segments with >10% N-content removed

## Data Structure

Each segment contains:
- `chromosome`: Chromosome identifier
- `start`: Start position (0-based)
- `end`: End position (exclusive)
- `sequence`: DNA sequence (16,384 bp)
- `strand`: Strand orientation (always "+")
- `n_content`: Fraction of N bases (ambiguous nucleotides)

## Usage

```python
from datasets import load_dataset

# Load the dataset
dataset = load_dataset("harari/human_grch38_segment")

# Access a segment
segment = dataset['train'][0]
print(f"Chromosome: {segment['chromosome']}")
print(f"Position: {segment['start']}-{segment['end']}")
print(f"Sequence length: {len(segment['sequence'])}")
```

## Intended Use

This dataset is designed for:
- Training Sparse Autoencoders on genomic sequences
- Analyzing DNA sequence patterns with foundation models
- Genomic representation learning
- Evo2 model feature extraction and interpretation

## Citation

If you use this dataset, please cite the original GRCh38 reference genome and GENCODE annotations:

```
@article{grch38,
  title={The reference genome sequence of the human genome},
  journal={Nature},
  year={2013}
}

@article{gencode,
  title={GENCODE: the reference human genome annotation},
  journal={Genome Research},
  year={2012}
}
```

## Data Source

- Reference genome: GENCODE GRCh38.p13 Release 41
- URL: https://www.gencodegenes.org/human/release_41.html
- Processing: Sliding window chunking with N-content filtering

## Preprocessing

1. Downloaded GRCh38.primary_assembly.genome.fa.gz
2. Extracted 16,384 bp segments with 4,096 bp stride
3. Filtered segments with >10% N-content
4. Added genomic coordinates and metadata

## License

This dataset is released under CC-BY-4.0 license, consistent with the GENCODE data usage terms.