---
language:
  - en
pretty_name: "NTv3 tutorial dataset - Genome & functional tracks"
tags:
  - 🧬 genomics
  - 📊 bigwig / functional tracks
  - 🎯 regression
  - ⚡ fine-tuning
  - 🧪 sequence-to-signal
  - 📐 functional-genomics
  - 🔬 bioinformatics
task_categories:
  - other
size_categories:
  - 100K<n<1M
license: cc-by-nc-4.0
---

# NTv3 Benchmark Dataset

This dataset contains the functional tracks and genome annotations used in the NTv3 benchmark evaluation.

## Dataset Organization

The dataset is organized as follows:

```
InstaDeepAI/NTv3_benchmark_dataset/
├── <species>/
│   ├── functional_tracks/
│   │   ├── <track_name>.bigwig
│   │   └── ...
│   └── genome_annotation/
│       ├── <track_name>.bed
│       └── ...
```

## Available Species

- **arabidopsis**
- **chicken**
- **cattle**
- **human**
- **maize**
- **rice**
- **tomato**

## Downloading Files

You can download files directly using their URLs:

```python
from huggingface_hub import hf_hub_download
import requests

# Download a BigWig file
bigwig_path = hf_hub_download(
    repo_id="InstaDeepAI/NTv3_benchmark_dataset",
    filename="human/functional_tracks/ENCSR628PLS.bigwig",
    repo_type="dataset"
)

# Download a BED file
bed_path = hf_hub_download(
    repo_id="InstaDeepAI/NTv3_benchmark_dataset",
    filename="human/genome_annotation/exon.bed",
    repo_type="dataset"
)
```

### Direct URL Access

You can also construct direct URLs to download files:

```python
import requests

# Construct URL
base_url = 'https://huggingface.co/datasets/InstaDeepAI/NTv3_benchmark_dataset/resolve/main'
file_path = "human/functional_tracks/ENCSR628PLS.bigwig"
url = f"{base_url}/{file_path}"

# Download file
response = requests.get(url)
with open("local_file.bigwig", "wb") as f:
    f.write(response.content)
```

## Available Tracks

### Human

#### Functional Tracks

Files are named by their S3 track ID (file_id). The mapping from track ID to track description can be found in the benchmark documentation.

- `human/functional_tracks/ENCSR628PLS.bigwig` (GM18861_chromatin_accessibility)
- `human/functional_tracks/ENCSR487QSB.bigwig` (GM18907_chromatin_accessibility)
- `human/functional_tracks/ENCSR410DWV.bigwig` (motor_neuron_chromatin_accessibility)
- `human/functional_tracks/ENCSR325NFE.bigwig` (bile_duct_chromatin_accessibility)
- `human/functional_tracks/ENCSR814RGG.bigwig` (ureter_chromatin_accessibility)
- `human/functional_tracks/ENCSR863PSM.bigwig` (BLaER1_H3K4me1)
- `human/functional_tracks/ENCSR682BFG.bigwig` (motor_neuron_H3K4me1)
- `human/functional_tracks/ENCSR754DRC.bigwig` (motor_neuron_H3K27ac)
- `human/functional_tracks/ENCSR962OTG.bigwig` (motor_neuron_H3K4me3)
- `human/functional_tracks/ENCSR046BCI_M.bigwig` (A673_PROcap_minus)
- `human/functional_tracks/ENCSR046BCI_P.bigwig` (A673_PROcap_plus)
- `human/functional_tracks/ENCSR100LIJ_M.bigwig` (Caco-2_PROcap_minus)
- `human/functional_tracks/ENCSR100LIJ_P.bigwig` (Caco-2_PROcap_plus)
- `human/functional_tracks/ENCSR935RNW_M.bigwig` (Calu3_PROcap_minus)
- `human/functional_tracks/ENCSR935RNW_P.bigwig` (Calu3_PROcap_plus)
- `human/functional_tracks/ENCSR114HGS_M.bigwig` (K562_PROcap_minus)
- `human/functional_tracks/ENCSR114HGS_P.bigwig` (K562_PROcap_plus)
- `human/functional_tracks/ENCSR799DGV_M.bigwig` (MCF10A_PROcap_minus)
- `human/functional_tracks/ENCSR799DGV_P.bigwig` (MCF10A_PROcap_plus)
- `human/functional_tracks/ENCSR154HRN_M.bigwig` (K562_HNRNPA1_eCLIP_minus)
- `human/functional_tracks/ENCSR154HRN_P.bigwig` (K562_HNRNPA1_eCLIP_plus)
- `human/functional_tracks/ENCSR249ROI_M.bigwig` (K562_HNRNPC_eCLIP_minus)
- `human/functional_tracks/ENCSR249ROI_P.bigwig` (K562_HNRNPC_eCLIP_plus)
- `human/functional_tracks/ENCSR321PWZ_M.bigwig` (K562_SRSF1_eCLIP_minus)
- `human/functional_tracks/ENCSR321PWZ_P.bigwig` (K562_SRSF1_eCLIP_plus)
- `human/functional_tracks/ENCSR484LTQ_M.bigwig` (K562_NCBP2_eCLIP_minus)
- `human/functional_tracks/ENCSR484LTQ_P.bigwig` (K562_NCBP2_eCLIP_plus)
- `human/functional_tracks/ENCSR862QCH_M.bigwig` (K562_U2AF1_eCLIP_minus)
- `human/functional_tracks/ENCSR862QCH_P.bigwig` (K562_U2AF1_eCLIP_plus)
- `human/functional_tracks/ENCSR527JGN_M.bigwig` (BLaER1_gene_expression_minus)
- `human/functional_tracks/ENCSR527JGN_P.bigwig` (BLaER1_gene_expression_plus)
- `human/functional_tracks/ENCSR701YIC.bigwig` (motor_neuron_gene_expression)
- `human/functional_tracks/ENCSR619DQO_M.bigwig` (ureter_gene_expression_minus)
- `human/functional_tracks/ENCSR619DQO_P.bigwig` (ureter_gene_expression_plus)

#### Genome Annotations

- `human/genome_annotation/exon.bed` (exon)
- `human/genome_annotation/intron.bed` (intron)
- `human/genome_annotation/splice_acceptor.bed` (splice_acceptor)
- `human/genome_annotation/start_codon.bed` (start_codon)

### Chicken

#### Functional Tracks

- `chicken/functional_tracks/ERX9662174.bigwig` (bone_marrow_chromatin_accessibility)
- `chicken/functional_tracks/ERX9662188.bigwig` (bone_marrow_gene_expression)
- `chicken/functional_tracks/ERX9662177.bigwig` (heart_chromatin_accessibility)
- `chicken/functional_tracks/ERX9662190.bigwig` (heart_gene_expression)
- `chicken/functional_tracks/ERX9662178.bigwig` (kidney_chromatin_accessibility)
- `chicken/functional_tracks/ERX9662192.bigwig` (kidney_gene_expression)
- `chicken/functional_tracks/ERX9662183.bigwig` (testis_chromatin_accessibility)
- `chicken/functional_tracks/ERX9662196.bigwig` (testis_gene_expression)
- `chicken/functional_tracks/ERX9662185.bigwig` (thymus_chromatin_accessibility)
- `chicken/functional_tracks/ERX9662198.bigwig` (thymus_gene_expression)
- `chicken/functional_tracks/ERX9662186.bigwig` (trachea_chromatin_accessibility)
- `chicken/functional_tracks/ERX9662200.bigwig` (trachea_gene_expression)
- `chicken/functional_tracks/ERX9662180.bigwig` (uterus_chromatin_accessibility)
- `chicken/functional_tracks/ERX9662194.bigwig` (uterus_gene_expression)

### Arabidopsis

#### Functional Tracks

- `arabidopsis/functional_tracks/SRR13808079.bigwig` (flower_mature_riboseq)
- `arabidopsis/functional_tracks/SRR13808080.bigwig` (flower_mature_riboseq_2)
- `arabidopsis/functional_tracks/SRR13808081.bigwig` (fruit_mature_riboseq)
- `arabidopsis/functional_tracks/SRR13808084.bigwig` (root_mature_riboseq)

### Rice

#### Functional Tracks

- `rice/functional_tracks/SRR13808064.bigwig` (leaf_V2_stage_riboseq)
- `rice/functional_tracks/SRR13808065.bigwig` (leaf_V2_stage_riboseq_2)
- `rice/functional_tracks/SRR13808066.bigwig` (leaf_booting_stage_riboseq_2)
- `rice/functional_tracks/SRR13808067.bigwig` (leaf_booting_stage_riboseq)
- `rice/functional_tracks/SRR13808068.bigwig` (root_V2_stage_riboseq)
- `rice/functional_tracks/SRR13808069.bigwig` (seedling_V2_stage_riboseq)
- `rice/functional_tracks/SRR13808070.bigwig` (sheath_V2_stage_riboseq)
- `rice/functional_tracks/SRR13808072.bigwig` (sheath_V2_stage_riboseq_2)
- `rice/functional_tracks/SRR13808073.bigwig` (sheath_booting_stage_riboseq)
- `rice/functional_tracks/SRR13808074.bigwig` (sheath_booting_stage_riboseq_2)
- `rice/functional_tracks/SRR13808075.bigwig` (spikelet_booting_stage_riboseq)
- `rice/functional_tracks/SRR13808076.bigwig` (spikelet_booting_stage_riboseq_2)
- `rice/functional_tracks/SRR13808077.bigwig` (stem_booting_stage_riboseq)
- `rice/functional_tracks/SRR13808078.bigwig` (stem_booting_stage_riboseq_2)

### Maize

#### Functional Tracks

- `maize/functional_tracks/SRR13808051.bigwig` (ear_V12_stage_riboseq)
- `maize/functional_tracks/SRR13808052.bigwig` (ear_V12_stage_riboseq_2)
- `maize/functional_tracks/SRR13808056.bigwig` (root_14days_riboseq)
- `maize/functional_tracks/SRR13808058.bigwig` (seedling_14days_riboseq)
- `maize/functional_tracks/SRR13808059.bigwig` (stem_14days_riboseq)
- `maize/functional_tracks/SRR13808061.bigwig` (stem_14days_riboseq_2)
- `maize/functional_tracks/SRR13808062.bigwig` (tassel_V12_stage_riboseq)
- `maize/functional_tracks/SRR13808063.bigwig` (tassel_V12_stage_riboseq_2)

### Tomato

#### Functional Tracks

- `tomato/functional_tracks/SRX27799703.bigwig` (fruit_0DPA_chromatin_accessibility)
- `tomato/functional_tracks/SRX29291440.bigwig` (fruit_0DPA_MicroTom_gene_expression)
- `tomato/functional_tracks/SRX29291439.bigwig` (fruit_0DPA_MicroTom_gene_expression_2)
- `tomato/functional_tracks/SRX29291438.bigwig` (fruit_0DPA_MicroTom_gene_expression_3)
- `tomato/functional_tracks/SRX27799731.bigwig` (fruit_10DPA_chromatin_accessibility)
- `tomato/functional_tracks/SRX29291448.bigwig` (fruit_10DPA_MicroTom_gene_expression)
- `tomato/functional_tracks/SRX29291447.bigwig` (fruit_10DPA_MicroTom_gene_expression_2)
- `tomato/functional_tracks/SRX29291446.bigwig` (fruit_10DPA_MicroTom_gene_expression_3)
- `tomato/functional_tracks/SRX29291431.bigwig` (fruit_15DPA_MicroTom_gene_expression)
- `tomato/functional_tracks/SRX29291430.bigwig` (fruit_15DPA_MicroTom_gene_expression_2)
- `tomato/functional_tracks/SRX29291445.bigwig` (fruit_15DPA_Wild_LA1781_gene_expression)
- `tomato/functional_tracks/SRX29291442.bigwig` (fruit_15DPA_Wild_LA1781_gene_expression_2)
- `tomato/functional_tracks/SRX27799722.bigwig` (fruit_3DBA_chromatin_accessibility)
- `tomato/functional_tracks/SRX27799719.bigwig` (fruit_3DPA_chromatin_accessibility)
- `tomato/functional_tracks/SRX27799727.bigwig` (fruit_5DPA_chromatin_accessibility)
- `tomato/functional_tracks/SRX29291444.bigwig` (fruit_5DPA_MicroTom_gene_expression)
- `tomato/functional_tracks/SRX29291443.bigwig` (fruit_5DPA_MicroTom_gene_expression_2)
- `tomato/functional_tracks/SRX29291441.bigwig` (fruit_5DPA_MicroTom_gene_expression_3)
- `tomato/functional_tracks/SRX27799718.bigwig` (fruit_7DPA_chromatin_accessibility)
- `tomato/functional_tracks/SRX27799733.bigwig` (leaf_chromatin_accessibility)

#### Genome Annotations

- `tomato/genome_annotation/exon.bed` (exon)
- `tomato/genome_annotation/intron.bed` (intron)
- `tomato/genome_annotation/splice_acceptor.bed` (splice_acceptor)
- `tomato/genome_annotation/start_codon.bed` (start_codon)

### Cattle

#### Genome Annotations

- `cattle/genome_annotation/exon.bed` (exon)
- `cattle/genome_annotation/intron.bed` (intron)
- `cattle/genome_annotation/splice_acceptor.bed` (splice_acceptor)
- `cattle/genome_annotation/start_codon.bed` (start_codon)

## Track Information

### Functional Tracks

Functional tracks include:
- Chromatin Accessibility tracks
- Histone modifications (H3K4me1, H3K4me3, H3K27ac)
- Transcription initiation (PRO-cap)
- RNA binding sites (eCLIP)
- Gene Expression
- mRNA translation (Ribo-seq)

### Genome Annotations

Genome annotation tracks include:
- Exon
- Intron
- Splice Acceptor
- Start Codon

## Notes

- BigWig files can be read using libraries like `pyBigWig`
- BED files can be read using `pyranges` or `pandas`
- All tracks are in the same coordinate system as specified in the benchmark