Discarded samples from rarefaction reason/solution/occurence

Hi! Just wondering what are some main reasons that some samples have low sequence counts so that it is discarded during rarefaction. Is it more likely to be a low biomass problem during sampling or just the random nature of high throughput sequencing? Are there any solutions around this problem? Also, for people who actually had experience with multiple projects, how common is it you end up losing some sample due to rarefaction.

Hi! It can be the nature of your samples - in some niches there are not a lot of biota at all. Then you need to find a way to increase a concentration of yielded DNA. It also can be a poor laboratory work or low quality of reagents / solutions. Also once manufacturer replaced our Illumina machine which was out of the order, which resulted in low amount of reads in samples.