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  • Welcome to the CLIP Forum
  • Experimental
    • Cell lysis
    • SDS-Page
    • Crosslinking
    • On-bead biochemistry
    • Adapters and Primers
    • Alternative cDNA library prep protocols
    • cDNA purification
    • Enzymes
    • PCR Products
    • qPCR
    • Illumina Sequencing
    • miCLIP (methylation iCLIP)
    • CLIP-rtPCR (site-specific analysis)
    • iiCLIP protocol
  • Computational
    • Demultiplexing
    • Use of random barcode in data analysis
    • Mapping to repetitive elements/RNAs
    • Differential CLIP binding analysis
  • To be Answered
  • References
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To be Answered

  • How to accurately compare two CLIP libraries of the same RBP with ~10-fold difference of CLIPped RBP abundance in the cell? How can we account for RBP/target RNA ratio?

  • Is it necessary to use spike ins, and if so, what kind of spike ins and how should I analyse this?

  • How do I choose/remove redundant annotations from genome annotation files?

  • How can I compare multiple RBP baits with different IP efficiencies?

  • What are the best ways to access and analyze published CLIP data?

  • What available pipelines are out there for analysing different CLIP datasets (iCLIP & PAR-CLIP)? Are there advantages/disadvantages to different established pipelines?

  • Which statistical methods are best at identifying cross-link sites?

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Last updated 3 years ago

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