domains / families / science / clip-peak-calling

clip-peak-calling

separate

Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

When to use

• Calling protein-RNA binding sites from CLIP-seq BAM
• Choosing between coverage-based, HMM-based, beta-binomial, and crosslink-site-based callers
• Applying ENCODE eCLIP thresholds
• Deciding when SMInput is mandatory
• Reconciling peak-set discordance between callers

Skill page

Source