query on filtering/dropping samples based on total reads (yield)

Question

[prasundutta87]

Hi,

This must be a pretty straightforward question, but just wanted the views of the community. We have sequenced (paired-end) multiple samples in a target enrichment experiment, and the samples have variable number of total reads. What should be the best way to filter samples by taking an informed decision? Is there some other metric that needs to be checked as well?

Regards, Prasun