hello,everyone! i am new to qiime ! here i have a problem that trouble me a long time.
when i do the deblur, i don't know how to choose the number of trim-length, because according to my demux.qzv, the minimum reads is low further to the highest reads. so i don't know the minimum value or the maximum value that i can choose.
i hope someone who master in it can solve me. thanks for your reading!!
In general, it is recommended to set --p-trim-length to a length where the median quality score begins to drop too low. There isn't a hard and fast rule for where to trim, but a good rule of thumb for your quality scores (although this isn’t a strict rule, it's a suggestion) is median quality scores around or above 30.
Another good indicator of where to trim is if you see a large drop in the quality scores for your reads. It looks like the lower whiskers of your quality scores do drop off around ~190 nt, but you'll want to take a look at the actual median values for that region (and the rest of your plot) to confirm. You can zoom in on your interactive quality plot to examine a section in greater detail by clicking and dragging your mouse over the segment you'd like to take a look at.
Here's a video from our Youtube channel that discusses examining interactive quality plots, and how to make these kinds of decisions when denoising your data - this may be helpful for additional context on how to choose the correct trim/trunc lengths for your data.