CRISPR screening analysis using mageck

Question

[Folder40g]

Hi

I've some fastq of a CRISPR screening analysis, with replicas. I'm doing some testing before the analysis. I've done it twice -removing and keeping the adapters-, in both cases when I used the option mageck count there is a warning that shows up in the screen for most of the samples. All fastq have between 19 and 23 millions reads.

Total tested reads: 100001, mapped: 37091(0.37090629093709065) 
WARNING @ Thu, 30 Aug 2017 13:05:38: Only 37.09062909370907 % of the reads can be identified.

For most of the samples, the percentage of reads idenfied fall below 40%, which to me seems a very low number. Any guess?

Thanks