This is not entirely true, for the reasons I explained. Also, cutadapt is often used to simply remove the primer sequences from the reads. That is, enter in the PCR primer sequence in 5' - 3' direction for the forward and reverse primers. There are many examples in the forum on this specific use case.
See the following:
Hi @elsamdea
These are good questions! You are correct... technically you can go either way... that is use cutadapt, or just trim the primers out directly within deblur or DADA2.
I prefer to use cutadapt to remove primers for the following reasons, which I think I've echoed elsewhere in the forum a few times:
There may be spurious off-target sequences within your data. Just trimming will retain these reads.
PCR / sequencing errors can add or remove bases from the beginning or end. Thus pote…
Hi @mohsen_ej , if you search the forum, you'll come across many examples of how to use cutadapt. There are quite a variety of ways to leverage this tool.
You'll likely just want to specify your specific primer sequences not the entire construct. That is, your primers are likely these (anything after the ...GAGACAG):
--p-front-f CCTACGGGNGGCWGCAG \
--p-front-r GACTACHVGGGTATCTAATCC \
Here are a couple to get you started:
-Mike
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