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---
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.
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