When I use the default of error rate (0.1) in cutadapt, I found that about 95% reads with adapter. When I use 0.3 of error rate, I found that 100% reads with adapter. I want to know which option is better? The primer detected with five mismatch is the right primer or the interesting 16S DNA sequences?
Thank you ！
95%is a good result.I do not think you still need to change the error rate to 0.3.With high sequencing depth you can just discard the un-alignment sequence.
16S Amplication is a PCR-based method so it will caused error (indel or substitute)in primer-region for many reason.Perhaps choose a better Hi-Fi enzyme may increase the performance.
You can also choose another way to cut off the primer by trimming a fixed base length with each read using command `vsearch --fastx_filter FN --fastq-minlen INT
hhhhhhh @sixvable Thank you very much！Zhong wen shi wo jue de fei chang qin qie！
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