Update README.md

README.md

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----
-license: mit
----
+---
+license: mit
+tags:
+- transcription-factor
+- binding
+- chipexo
+- genomics
+- biology
+pretty_name: Rossi ChIP-exo 2021
+configs:
+- config_name: metadata
+  description: Metadata describing the tagged regulator in each experiment
+  default: true
+  data_files:
+  - split: train
+    path: rossi_2021_metadata.parquet
+  dataset_info:
+    features:
+    - name: regulator_locus_tag
+      dtype: string
+      description: Systematic gene name (ORF identifier) of the transcription factor
+    - name: regulator_symbol
+      dtype: string
+      description: Standard gene symbol of the transcription factor
+    - name: run_accession
+      dtype: string
+      description: GEO run accession identifier for the sample
+    - name: yeastepigenome_id
+      dtype: string
+      description: Sample identifier used by yeastepigenome.org
+- config_name: genome_map
+  description: ChIP-exo 5' tag coverage data partitioned by sample accession
+  data_files:
+  - split: train
+    path: genome_map/*/*.parquet
+  dataset_info:
+    features:
+    - name: chr
+      dtype: string
+      description: Chromosome name (e.g., chrI, chrII, etc.)
+    - name: pos
+      dtype: int32
+      description: Genomic position of the 5' tag
+    - name: pileup
+      dtype: int32
+      description: Depth of coverage (number of 5' tags) at this genomic position
+language:
+- en
+---
+
+# Rossi 2021
+
+This data is gathered from [yeastepigenome.org](https://yeastepigenome.org/). This work was published in
+
+[Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, Kuzu G, Bocklund K, Farrell NP, Blanda TR, Mairose JD, Basting AV, Mistretta KS, Rocco DJ, Perkinson ES, Kellogg GD, Mahony S, Pugh BF. A high-resolution protein architecture of the budding yeast genome. Nature. 2021 Apr;592(7853):309-314. doi: 10.1038/s41586-021-03314-8. Epub 2021 Mar 10. PMID: 33692541; PMCID: PMC8035251.](https://doi.org/10.1038/s41586-021-03314-8)
+
+## Dataset details
+
+`genome_map` is fully reprocessed data from the sequence files. I used the nf-core/chipseq pipeline, details for which can be found in `scripts/`. With
+those bams, I filtered the reads using `samtools` and the same settings specified in Rossi et al 2021, and then counted 5' ends using bedtools. See
+`scripts/count_tags.sh`.
+
+## Data Structure
+
+### Metadata
+
+| Field                 | Description                                                       |
+|-----------------------|-------------------------------------------------------------------|
+| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the transcription factor |
+| `regulator_symbol`    | Standard gene symbol of the transcription factor                  |
+| `run_accession`       | GEO run accession identifier for the sample                       |
+| `yeastepigenome_id`   | Sample identifier used by yeastepigenome.org                      |
+
+### Genome Map
+
+| Field    | Description                                                    |
+|----------|----------------------------------------------------------------|
+| `chr`    | Chromosome name, ucsc (e.g., chrI, chrII, etc.)                |
+| `pos`    | Genomic position of the 5' tag                                 |
+| `pileup` | Depth of coverage (number of 5' tags) at this genomic position |
+
+## Usage
+
+The entire repository is large. It may be preferable to only retrieve specific files or partitions.
+You can use the metadata files to choose which files to pull.
+
+```python
+from huggingface_hub import snapshot_download
+import duckdb
+import os
+
+# Download only the metadata first
+repo_path = snapshot_download(
+    repo_id="BrentLab/rossi_2021",
+    repo_type="dataset",
+    allow_patterns="rossi_2021_metadata.parquet"
+)
+
+dataset_path = os.path.join(repo_path, "rossi_2021_metadata.parquet")
+conn = duckdb.connect()
+meta_res = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10", [dataset_path]).df()
+print(meta_res)
+```
+
+We might choose to take a look at the file with accession SRR11466106:
+
+```python
+# Download only a specific sample's genome coverage data
+repo_path = snapshot_download(
+    repo_id="BrentLab/rossi_2021",
+    repo_type="dataset",
+    allow_patterns="genome_map/accession=SRR11466106/*.parquet"
+)
+
+# Query the specific partition
+dataset_path = os.path.join(repo_path, "genome_map")
+result = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10", 
+                     [f"{dataset_path}/**/*.parquet"]).df()
+print(result)
+```