Hi,
I sequenced total 80 samples for the same species of insect gut, the sequencing result shows me a high range.
The lowest sequence read is just 877
(the lowest 10 reads are 877, 1082, 1469, 2256, 2535, 3085, 4099, 4340, 5085, 5796).
The highest read is 222380
(the highest 10 reads are 222380, 182650, 180804, 154292, 133869, 129672, 107876, 86917, 76685, 73799).
I get a hard time picking the sampling depth value because no matter the value I pick I get a very low “retained (%) feature" value. -- around 20%.
Is that mean my sequencing depth is low?
How import for "retained (%) feature" value for further analyzing steps?
You are not alone! This is hard choice because you are facing a trade-off between keeping more samples or keeping more depth in each sample, and you want to do both!
Check out these discussion of the issue, and let us know what you decide to do
