Hello! I am stuck with one thing. I am using QIIME2 for my 16S Anslysis. I am trying to filter reads in the denoising step and I am getting the representative sequence set which i am not able to understand. I hereby share some stats of the denoising step performed using dada2 in the table below:
Trunc-Len Reads Non-Chimeric Sequences 0 420355 1946 40 52320 1308 100 455600 4556 200 104200 3521 300 2400 8
As per what I understood, it is filtering out the bases above the the given trunc length.
What I don’t understand is why it is also not considering those reads which are less than the given trunc length. It only considers the reads with length more the the trunc length provided and truncates the remaining bases. Also, I do not understand, why the representative sequnces set is of the exact length as that of the trunc length. Whatever the trunc length is given, the representative set becomes of that length exactly as the trunc length.
I dont understand why this is happening. What can be the consequences of these in terms of assigning the taxonomy specially in case of de-novo based method.
Please help me learn and understand the parameter so that I can proceed with the elaborate knowledge in order to analyse my data correctly.
Thanks to all of you in advance for helping me understand the pararmeter.
Best Regards, Rahul