Is it possible to find the mutation in RNA-seq reads?

Question

[PK]

Hi all,

I am analysing the CLIP-Seq data. The protocol follows UV treatment to identify the protein RNA-interaction so i am introducing a mutation. So my question is there any way to identify these mutations. If the question is not clear please ask me?

Answer 1

[Carlo Yague]

The mutation footprint induced by the UV-crosslink in CLIP and PAR-CLIP experiments is used as a proxy for protein binding in multiple tools, including:

• PIPE-CLIP (code, paper)
• PARalyzer (paper)
• WavClusterR (R package, paper)

I suggest that you read the papers and try to understand how they identify the mutations. If you have more specific questions, feel free to come back and ask for clarifications.