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!
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.