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clip-motif-analysis

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

When to use

• Discover RBP binding motifs
• Characterize RBP sequence specificity
• Register motifs to crosslink positions
• Validate in vivo CLIP motifs against in vitro RBNS Kd
• Reconcile motif disagreements across tools
• Correct for uracil crosslinking bias
• De novo motif discovery from peaks
• Positional k-mer enrichment analysis

When not to use

• Deep learning prediction of per-base affinity profiles
• Raw sequence to signal prediction

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