I have 2 NGS runs with 50 and 43 samples respectively.
I did the following:
- Trimmed off primers from my reads using cutadapt separately for two different runs
- denoised data with dada2 separately for two runs (Both the runs yielded slightly more than 2000 features)
- merged the 2 feature tables (obtained from dada2) (yielded a total feature of ~3700
- filtered sequences and features (removed features that occured in less than 3 samples)
- Now, I was left with 1165 features (after filtering) and I am heading towards taxonomic classification. Before I taxonomically classify these sequences I want to ask is getting 1165 features from 93 samples usual enough? or these are too huge or too less?
My samples are stool samples from cancer patients and I intend to study their microbiome composition