I have processed three batches of samples into three tables and now I want to combine these tables. The tables are from the same samples taken in different times, I have different names in each time ( e.g. T1P1_T0, T1P1_T1 and T1P1_T3) . What I did was to merged all the files before import them into Qiime2 and then I processed them as I did with each batch before with the same parameters with DADA2. But the results aren´t the same when I did the process individually (each batch) and when I did the process with all the reads in a unique batch. What I found reading the forum was that I have the option to merged the features tables and the rep-seqs files but I had the doubt about it. If I do the three batches individually isn´t the same if I merged the reads and apply the same process inside DADA2?
For example, the sequence counts individually are:
but when I processed all in a unique batch the sum of the T0_T1_T3 times are: 1.289.019 and it shoud be 1.278.928 ¿How can pass 10.091 seqs with the same quality process?
I attached the files :
table-16S-single-end-tiempo-3-20qs-180ml-180t-10trim.qzv (461.9 KB)
table-16S-single-end-tiempo-1-20qs-180ml-180t-10trim.qzv (436.3 KB)
table-single-end-t0-20qs-180ml-180t-10trim-1.qzv (439.1 KB)
table-single-end-t0-t1-t3-20qs-180ml-180t-10trim.qzv (579.1 KB)