benjjneb
commented
6 years ago Is it possible to analize these kind of sequences with DADA for generating ASV tables ?
Yes, outside of taxonomic assignment, nothing in DADA2 is specific to a particular gene.
if It is possible. How does the variability of the sequences affect the learning error? or should I cut all sequences to the same lenght ?
Assuming that is biological length variation, you're fine. Just make sure that you've removed any primers and adapters, which may require an outside program as the trimming in DADA2 doesn't support removing variable-length primers or primers at the ends of sequences.
My name is Paul Roldan Olarte and I am an undergrad student at Universidad El Bosque in Bogota, Colombia. I'm currently analyzing metabarcoding sequences in DADA2. These sequences correspond to plants (marker tRNL) and Eukaryota (marker 18S) and have a variable range of length from 50 to 150 bp.
My questions are:
Is it possible to analize these kind of sequences with DADA for generating ASV tables ?
if It is possible. How does the variability of the sequences affect the learning error? or should I cut all sequences to the same lenght ?
Thank you for your attention.
Paul Roldán Olarte Student of Bioengineering - Universidad El Bosque Bogota, Colombia