| --- |
| 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. |
|
|
