Low assigned reads

[juulluu21]

I have couple of pair ends reads. Average size of the libraries is 70 million (150nt paired end reads). However, only ~8% of the reads can be assigned to bacteria and virus (I used that index). Most of the reads remain as unassigned. Is it normal? Lots of the reads indeed are assigned to the host, but I am curious what % should map to bacteria/virus?

Thanks.

[mourisl]

That quite depends on the library preparation. If the cells are extracted from human, it is normal to see majority of the reads are from the host human.