How to train the classifier with mixed forward primers?
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Hi Colin,
I hope you are doing well! Thanks for sharing this useful tool!
I am analysing V1-V2 16S rRNA sequence data. I want to use qiime feature-classifier extract-reads to extract reads and train a classifier.
However, this data has mixed primers. I came across this one: How to train the classifier with multiple reverse primers? . Could you please help me to have a look?
V1-V2 MiSeq primers
Forward: These primers are mixed at a 4:1:1:1 ratio (28F-YM is the 4)
28F-YM: GAGTTTGATYMTGGCTCAG
28F-Borrellia: GAGTTTGATCCTGGCTTAG
28FChloroflex: GAATTTGATCTTGGTTCAG
28F-Bifdo: GGGTTCGATTCTGGCTCAG
28F-YM vs 28F-Borrellia == 3
28F-YM vs 28FChloroflex == 4
28F-YM vs 28F-Bifdo == 4
28F-Borrellia vs 28FChloroflex == 4
28F-Borrellia vs 28F-Bifdo == 4
28FChloroflex vs 28F-Bifdo == 6
(19-4) differences / 19 bp length == 78.95% similar
Another problem is these primers are mixed at a 4:1:1:1 ratio (28F-YM is the 4)? Should I use 28F-YM & --p-identity 0.7/0.8?
Any advices would be highly appreciated! Thanks!
Kind regards,
Birong
hello, please post all user support questions to the QIIME 2 forum. Thank you.
Sorry for this, I post it to QIIME 2 forum yesterday: How to train the classifier with multiple mixed forward primers? . Could you please have a look? Many thanks!