What to do with a *.bowtie CLIP-Seq dataset from GEO?

[bgarchow]

Hi all,

Dumb biologist here so please be gentle. I have a *.bowtie CLIP-Seq dataset downloaded from the NCBI GEO website and I have no idea what to do with it.

The experiment was immunoprecipitation of an RNA binding protein followed by RNA-Seq to sequence the RNA species bound (crosslinked) to it.

I would really appreciate it if someone could outline the steps I would need to take to extract meaningful data (i.e. a list of the bound RNA species and confidence values).

Thanks!