Typically how many CLIP reads can be mapped to genome?

Question

[yhu10thu]

Hi,guys,

I'm new to CLIP-seq study. I found some data from NCBI and try to map the date back to the genome. But I found only 10-20% of reads can be mapped to genome successfully. Is it normal?

Thanks

Yue

[yhu10thu]

By the way, I use bowtie and the parameter according to the original paper. The parameter allow for one mismatch and trim the first six nucleotides because they are barcode.