Problem of --cluster-size 1

[lalintao]

Dear Author, while using spacedust, when I wanted to keep the results with --cluster-size 1, I found that the results did not include those with num_hits equal to 1. I also tried setting -e 1000 to eliminate the influence of the E-value, but it still didn’t work. I would really like to discuss this issue with you and look forward to your reply!

[RuoshiZhang]

Hi! spacedust is designed to report only clusters with ≥ 2 hits. This is intentional, as the cluster match statistics does not apply to single-hit clusters, and unfortunately setting the evalue threshold does not affect the behavior. We will consider either enforcing a minimum cluster size of 2 or adding an explicit option for reporting single-hit clusters without the statistics.

[lalintao]

@RuoshiZhang Thank you for your reply. It has been extremely helpful for our research. We truly appreciate it!