GSE315406 eCLIP Data Processing

eCLIP geo_data_processing 4 steps

Publication

Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces.

Cell systems (2026) — PMID 42025161

Dataset

GSE315406

Comprehensive RNA-binding protein analyses using enhanced CLIP (ENCORE) [dataset2]

Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.

Processing Steps

Generate Jupyter Notebook
  1. 1

    eCLIP data processing pipeline (Skipper v1.99.0)

    Skipper v1.99.0
  2. 2

    Reads were trimmed, mapped to hg38 using STAR, deduplicated, and binding sites identified using beta-binomial model accounting for GC bias.

    STAR
  3. 3

    Reproducible enriched windows were identified at FDR < 0.2 across biological replicates.

  4. 4

    Library strategy: iCLIP

    iCLIP

Tools Used

Skipper STAR iCLIP
Raw Source Text 
Supplementary files format and content: Tab-delimited BED-like files containing reproducible enriched windows identified by eCLIP. Columns include: chromosome, start, end, feature type, enrichment odds ratio, p-value, FDR.
eCLIP data processing pipeline (Skipper v1.99.0)
Reads were trimmed, mapped to hg38 using STAR, deduplicated, and binding sites identified using beta-binomial model accounting for GC bias.
Reproducible enriched windows were identified at FDR < 0.2 across biological replicates.
Assembly: hg38
Supplementary files format and content: reproducible_enriched_windows.tsv.gz files contain reproducible enriched windows between two replicates (using uniquely mapped reads).
Supplementary files format and content: .bw files contain reads-per-million scaled read densities.
Library strategy: iCLIP
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