what is the optimal error rate of q2 cutadapt?

Dear all,
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 !

1 Like

Hi @Zhanzhan

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

我看到你的问题觉得你应该是宏基因组群里问这个问题的人 :joy: 刘老师扩增子培训班使用的方法就是后面这种切除固定长度的,你可以试下。用英文回答是因为论坛要求。

hhhhhhh @sixvable Thank you very much!Zhong wen shi wo jue de fei chang qin qie!


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