There are the times I have re-run some samples and got some improvement, like there were 3 taxa in first run and ~30 taxa in the second run.
And there are the times I dropped the sample because the sample which has low read count was in a group consists of like 6 samples, so there I had other good samples to continue with.
@colinbrislawn, are the samples of A and B from different runs? If not, why there is such a drop of read counts?
Thank you @jwdebelius, @colinbrislawn, I got the answer for what to do when this happens. But I would like to point the real problem even if it is a problem with the platform.
I believe this is about the platform because when I just re-run without changing anything or re-extraction, read count can jump from 2k to 100k. Plus, phred scores are getting worse and worse with each run.
I’m poking it this much because I don’t have the platform. If the reason is the platform, I would think that they are not taking a good care of it, and plan to change where I send the cartridge