Data Access
Broadly Consented Data Downloads
We provide access to broadly consented Fiber-seq data that can be used by researchers for various genomic studies.
Available Datasets
Our broadly consented datasets include the following samples:
- CHM1: Complete hydatidiform mole cell line
- CHM13: Complete hydatidiform mole cell line (GRCh38 alignment)
- CHM13_DSA: CHM13 data aligned against the DSA (T2Tv2.0)
- GM12878: Lymphoblastoid cell line from Coriell Cell Repository
- HG002: Human genome reference sample (Ashkenazi Jewish trio son)
- K562: Chronic myelogenous leukemia cell line
All samples are processed with FIRE (Fiber-seq Inferred Regulatory Elements).
Data Formats
All datasets are provided in standard formats:
- Fiber-seq CRAM files: Primary data format containing m6A calls and nucleosome positions
- Processed FIRE outputs: Summary statistics, peaks, and aggregated results
Download Instructions
Browse Available Data
You can explore all available samples using the AWS CLI:
aws s3 ls --no-sign-request --endpoint-url https://s3.kopah.uw.edu s3://stergachis/public/FIRE/broadly-consented/
Download Data
To download specific samples or datasets, use the AWS CLI with the following pattern:
aws s3 sync --no-sign-request --endpoint-url https://s3.kopah.uw.edu s3://stergachis/public/FIRE/broadly-consented/[SAMPLE_NAME]/ ./[LOCAL_DIRECTORY]/
For example, to download CHM13 data:
aws s3 sync --no-sign-request --endpoint-url https://s3.kopah.uw.edu s3://stergachis/public/FIRE/broadly-consented/CHM13/ ./CHM13_data/
Data Use Guidelines
When using our broadly consented data, please:
- Cite the original studies and data contributors
HPRCv2 Fiber-seq CRAMs
We also provide access to Fiber-seq CRAM for the HPRCv2 release. These CRAMs contain m6A calls, MSP calls, and nucleosome calls for each of the HPRCv2 samples with Fiber-seq data.
You can find these CRAMs in the following S3 bucket. Data is aligned both to the Donor Specific Assembly (dsa) and to GRCh38 (shared.ref).
aws s3 ls --no-sign-request --endpoint-url https://s3.kopah.uw.edu 's3://stergachis/public/HPRCv2/FIRE-bams/'
HPRCv2 FIRE Peaks
We provide pangenome graph-based union peak calls for the HPRCv2 Fiber-seq samples. These peaks are called on donor-specific assemblies and then projected to multiple coordinate systems. For full column definitions, thresholds, and methodology, see the README included in the bucket.
Available files
Union peaks (every sample × consensus peak that passes in at least one sample):
| File | Coordinates |
|---|---|
union-peaks-cons.bed.gz | Pangenome graph consensus (shown in T2T-CHM13 coords when possible) |
union-peaks-chm13.bed.gz | T2T-CHM13 reference paths |
union-peaks-asm.bed.gz | Per-sample assembly contigs |
union-peaks-hg38.bed.gz | GRCh38 liftover |
Called peaks (filtered to sites passing thresholds: FIRE coverage ≥ 4, fraction accessible ≥ 0.2):
| File | Coordinates |
|---|---|
peaks-cons.bed.gz | Pangenome graph consensus (shown in T2T-CHM13 coords when possible) |
peaks-chm13.bed.gz | T2T-CHM13 reference paths |
peaks-asm.bed.gz | Per-sample assembly contigs |
peaks-hg38.bed.gz | GRCh38 liftover |
All files are bgzipped BED files with a #chrom header line and tabix indices (.tbi).
Download
Browse available files:
aws s3 ls --no-sign-request --endpoint-url https://s3.kopah.uw.edu 's3://stergachis/public/HPRCv2/FIRE-peaks/'
Download all peak files:
aws s3 sync --no-sign-request --endpoint-url https://s3.kopah.uw.edu s3://stergachis/public/HPRCv2/FIRE-peaks/ ./FIRE-peaks/