Hello..
Can anyone enlight me, if sequences from different sequence run are to be imported and denoised separetly and later merged together ? If I merged all the sequnces from 3 different run and then subject the demux file to denoising, will that be approprite?
Thank you for your time.
Hello!
For dada2, the best approach would be to import each dataset separately, then run primers removal and dada2 for each run separately but with identical (!!!) parameters, or using exactly the same commands, and then merge output files like feature table and rep-seqs. Dada2 uses sequences to train the error model, so merging different runs may introduce biases in runs with a lesser number of reads.
For deblur, runs can be merged before denoising.
Best,