I donot know how to truncate paired sequence bases. How do we know about the quality of the bases is high or low?

In the demux.qzv quality plots, i.e . two quality plots one for forward and one for reverse. I donot know how to truncated both quality plots. I have attached the file. Please help me in sequence quality control I used the command as follows;qiime dada2 denoise-single
--i-demultiplexed-seqs demux.qza
--p-trim-left 0
--p-trunc-len 120
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza

Hi @Aqleem12,

Let me know if I’m misunderstanding your question, but in order to truncate both sides, you need to use qiime dada2 denoise-paired. This method will give parameters to control trim-left and trunc-len for both forward and reverse reads independently. Call qiime dada2 denoise-paired --help to learn more!

If your question is more about where/when to truncate your sequences, that is going to depend on your data, as there’s not really a magic number. Although your plots have very nice and consistent quality scores, so I would suspect that any reasonable trunc-len is probably going to give you nice results. You’ll have to play around with it to know for sure.

Dear Sir,

Thank you for your support. can i use the following format for that??
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux.qza
–o-table table
–o-representative-sequences rep-seqs
–p-trim-left-f 13
–p-trim-left-r 13
–p-trunc-len-f 150
–p-trunc-len-r 150

Yep, that’s the right command and parameters!

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