I am making custom database for functional gene arsM, for this I have downloaded arsM 71000 gene sequences from fun gene database.
To extract reference gene sequences I am using below command:
qiime feature-classifier extract-reads
How can I confirm that all these sequences contain these above arsM primer sequences and ref.seq.read.fa is extract according to primer sequences.
Is it possible to remove sequences which do not contain above primer sequences?
Thanks a lot for all your previous helps.
extract-reads will only output trimmed sequences from reads that contain the primers. So there is no need to confirm that the primers were in those sequences — they were there, but then were trimmed out and the internal region (simulated amplicon) output.
Thanks for your quick help. Do I also need to remove taxonomy for gene Id which are not present in the ref.seq.qza and can I know how many sequences are present in ref.seq.qza?
Try to use
feature-table tabulate-seqs. I am not sure, but it might list the number of sequences.
Thank you for your all help.
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