I have tried to use my own classifiers to assign the rep-seqs under Qiime2, but the ratio of “unassigned” sequences is still about 50%, which can not be assigned to kingdom.
I found the question was that my sequences in rep-seqs.qzaIE_rep-seqs.qza (3.3 MB) is not listed forwardly. The sequences which list reversely cannot be assignedIE_taxonomy5.qza (1.2 MB) . I also searched the unassigned sequences in NCBI and could find them at least genus-level classification.
So, I suspect the problem is the repetitive sequences do not list at the right way. What can I do to converts the DNA sequence into its reverse and make the repetitive sequences all forwardly?
I input data by
qiime tools import \
–type SampleData[PairedEndSequencesWithQuality] \
–input-path /media/sf_Qiime/Rawdata/Potexperiment/test/IEManifest.csv \
–output-path /media/sf_Qiime/Rawdata/Potexperiment/test/IE.qza \
Thanks in advance!