Hello, I am new to QIIME2. When using DADA2, does this remove the primer sequence? or do I need to first use the cutadapt pluggin?
Thanks for your help,
Holly
No need to use cutadapt! dada2 has a --p-trim-left parameter to trim a specified number of bases from the 5’ end of each sequence. If using the denoise-paired method for paired-end reads, there is a --p-trim-left-f and a --p-trim-left-r parameter to trim from the forward and reverse sequences, respectively. These parameters are primarily intended for trimming primers from the start of each sequence.
This relies on knowing precisely where the primer is, however. If the primer is not in the same position in each sequence (e.g., the first N bases of the 5’ end), you should use cutadapt to trim out primers.
I hope that helps!
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