I have 10 samples paired-end data and after importing it, I merged it by using vsearch merge-pairs. Then applied quality control to the sequences using quality-filter q-score. After that, I am proceeding with the deblur denoise-16S. But struggling with deciding the value for -p-trim length.
I am attaching here the demx-joined.qzv file demux-joined.qzv (297.2 KB)
. Please help me out in deciding the trim length value. It would be really helpful.
Though, I tried using trim length as 270 but received only three features in 6 samples. There was no feature reported in 4 other samples.
Selecting a trim length is something that will be different for everyone, depending on the dataset you are working with and what your analysis goals are. We cannot select this for you (please see our CoC guidelines on your work being your own).
With that being said, I'd recommend going through the Moving Pictures tutorial to help you better understand how to effectively select a trim length when denoising your data, and some general guidelines/recommendations for this. There are also many forum posts about this same question, which you can search for (something like 'selecting trim length for deblur') if you want additional references.
