Hi, thanks in advance.
This may be a simple question. Now I have 2 types of paired-end sequencing results: original FASTQ files and FASTQ files with barcodes and primers removed. Since I have to train a feature classifier for my data, and I noticed primer sequences are required, which type of data should I import to do taxonomy classification analysis?
I'm asking because I'm unsure if the primers are removed from my data, can the trained classifier recognize sequences correctly?
yes, primers are only needed to identify the exact region of the 16S gene in the database. You only provide it on the level of database creation.
They are not required for classification per se and should be trimmed before taxonomical classification of sequences.
By the way, I have imported my data, so now I can ignore the demultiplexing step and move on to denoising and clustering, right?
I don't know, I haven't seen your data. Demultiplexing is crucial, but its common that demultiplexed data gets shipped for analysis.
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