Which protocol to use For HITS-clip

[Cai Qi]

Hi Zhanglab:

I am new to CLIP-SEQ. I want to follow the protocols of CTK-toolkit to go through the pipeline for CLIP-SEQ.

I downloaded a HITS-Clip dataset from Robert Darnell lab(NOVAS-clip). However, in the CTK-toolkit website there are pipelines for iclip/parclip/eclip. I want to make sure which version should I follow for HITS-Clip in case I meet some problems in the middle and need to do it from beginning. I felt I need to follow PAR-clip protocol. But I want to make sure before beginning.

Thank you very much,