Is there a way to get the actual read sequences after clustering (feature table) by deblur?
I have the feature table (each sample has a frequency for a certain feature) I also have the sequences of the features. Now I want to get the clustered reads sequences. Is this feature supported?
Good afternoon,
When running deblur, you have the option of passing the --o-representative-sequences flag to output all ‘deblured’ reads. More info here:
https://docs.qiime2.org/2017.12/plugins/available/deblur/denoise-16S/
Does that sound like what you want? I’m not sure I understand your goal and I don’t want to lead you in the wrong direction.
Colin
Hi Colin,
I already have the file that you are pointing at, what is something similar. I need all the sequences read assigned to a certain OTU. I am searching for mutations so ai need all reads rather than only a representative seq.
Got it!
I’m not sure how to get all initial reads that were added to each deblured read. Let’s see what the qiime devs recommend. @wasade
Colin
@Nourhan_sahly, Deblur isn’t clustering per se but subtracting what appears to be read errors. As such, it may not be safe to interpret the surrounding reads as mutations. Perhaps you’re looking for something like Oligotyping?
Best,
Daniel
Sounds interesting!
Thanks for your time.
Nourhan
Hello Nourhan,
Like Daniel said, Deblur is trying to find and remove errors, so it might not be the right tool for identifying mutations.
One option would be to use deblur to remove errors, then use a method like vsearch to cluster your reads so that you can view collections of reads that are part of each OTU.
In any method you use, one core challenge will be distinguishing errors from mutations; biological mistakes (mutations) will look a lot like sequencing mistakes (errors), so it’s hard to tell them apart.
I hope you find a good solution!
Colin
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