What percentage should I use?

[SDPA_Pet]

Hi, I have some results from BLASTX. If I set % of identity to 60%, I will loss more than 50% of reads (results), compare to identity cutoff to 30%.

Should I use 30%? Is there any rule of thumb? I just don't want the future reviewer think the cutoff is too low. At the mean time, I really don't want the cutoff too high to lose 50% information of my metagenomic information.

Thanks,

[yzzhang]

What is the coverage cutoff? and what is the database? I think you can check the parameters used in previous papers and MG-RAST is using