Hello everybody, this is my first post, but i have been following the forum for a couple of months.
When i use cutadapt to trim my primers, some of the sequences do not get the primer trimmed, because my primer in my metadata file is GATAYTGGGYDTAAAGNG and some of the sequences instead of having an Y that should mean a G or C, they have an A or T, so the plugin doesnt recognice it.
Does this means that the sequence is bad quality?
My question is about understanding what to do, is it ok if instead of using cutadapt I use dada2 trim-left and just cut the primer length from all my sequences?
Or should I think that those sequences are bad quality and I need to take them out from the analysis? (in that case, how can i do that).
The same happens with my reverse primer.
Thank you in advance.