I am currently a novice at bioinformatics and want to ensure that I'm doing my analysis correctly. Please let me know what option is correct:
- Use decontam first before importing into Qiime 2
- Use the output table from 'qiime dada2 denoise-paired' and input that into decontam
- Complete full taxonomic classification and differential abundance analysis with negative controls included in the data and then use the feature table in decontam
Thank you in advance for your help!