TE-Seq Data v1
Transposable Element locus sequences from the human genome (GRCh38).
Dataset Summary
| Property | Value |
|---|---|
| Total records | 4,693,511 |
| File size | ~894 MB |
| Sequence column | sequence (consume verbatim; no padding trimming) |
| Labels | family (1,180 unique), class (13 unique) |
Schema
| Column | Type | Description |
|---|---|---|
sequence |
string | DNA sequence (consume as-is) |
family |
string | TE family label (primary training target) |
class |
string | TE class (e.g., SINE, LINE, LTR, DNA) |
chrom, start, end |
string/int | Genomic coordinates |
strand |
string | + or - |
subfamily |
string | Subfamily label |
| Other columns | Locus metadata (ID, loci, group, N1, N2, TE_chrom, TE_start, TE_end) |
File Status: Corrected Splits vs Legacy Root
Use the corrected split shards for all current DeepGenopix training, simulator, and benchmark jobs:
train/te_seqdata.parquetval/te_seqdata.parquettest/te_seqdata.parquetsplit_summary.jsonte_seqdata.recovered.parquetfor corrected raw sibling access
Do not use the root te_seqdata.parquet for new jobs. It is retained only as a legacy snapshot for backward compatibility and was intentionally left untouched when the corrected split was uploaded. The corrected split excludes the remaining 405 unresolved unlabeled rows.
Current canonical split-input revision for reproducible jobs: f107d46c5a61087eb3fb19b4e3e75fdef0b74fdd.
Usage
Use this dataset as the raw input for run_parquet_etl() in DeepGenopix:
from deepgenopix.etl import run_parquet_etl
run_parquet_etl(
"te_seqdata.parquet",
output_dir="data/processed/te_visuals/<run_id>",
sequence_col="sequence",
label_col="family", # or "class"
)
Class Distribution
- SINE: 1,770,903
- LINE: 1,516,226
- LTR: 720,177
- DNA: 483,994
- Satellite: 7,018
- Other: ~2,000 each or fewer
Splits
The ETL builds stratified train/val/test splits automatically:
- Tier 1 (< 30 samples): all → train
- Tier 2 (30–200): floor-20 val, 10% test, rest → train
- Tier 3 (> 200): 10% val, 10% test, rest → train