I have got paired reads from the company. The sequence base for each forward and reverse read was 300. Then I use Greengenes (16S rRNA) 13.8 MARKER GENE DATABASE USING FOLLOWING COMMANDS TO TRAIN CLAISSIFIER BY USING THE FOLLOWING COMMANDS;
qiime feature-classifier extract-reads –i-sequences 99_otus.qza –p-f-primer CCTACGGRRBGCASCAGKVRVGAAT –p-r-primer GGACTACNVGGGTWTCTAATCC –p-trunc-len 300 –o-reads ref-seqs.qza I don’t know whether I am wrong or right, Please help me to train a classifier for my paired end reads. I
With 2x300bp reads you should be covering most of your amplicon. You should know what's the length of the sequence amplified by your primers. That number minus the number of bases of the primers (25+22 in your case) would be the number to use in -p-trunc-len (XXX below). With the first command you extract the sequences to train your classifier from the database. qiime feature-classifier extract-reads –i-sequences 99_otus.qza –p-f-primer CCTACGGRRBGCASCAGKVRVGAAT –p-r-primer GGACTACNVGGGTWTCTAATCC –p-trunc-len XXX –o-reads ref-seqs.qza
Then you actually train the classifier using the sequences you just extracted.
qiime feature-classifier fit-classifier-naive-bayes \ --i-reference-reads ref-seqs.qza \ --i-reference-taxonomy ref-taxonomy-99.qza \ --o-classifier classifier.qza
After denoise the trunk lenght for forward and reverse read was: 300 each..
Today one of the leader of QIIME2 has told me to use the following commands?
qiime feature-classifier extract-reads \
--i-sequences 99_otus.qza \
--p-f-primer CCTACGGRRBGCASCAGKVRVGAAT \
--p-r-primer GGACTACNVGGGTWTCTAATCC \
--o-reads ref-seqs.qza
Five hours have passed and I donot know what to do. Hope any other suggestions
Did you try it? That should work. That command will extract sequences from your database, and after that you should train your classifier with:
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ref-seqs.qza --i-reference-taxonomy ref-taxonomy-99.qza --o-classifier classifier.qza
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