I am wondering if anyone can suggest me if dada2 command is correct for the ITS data processing.
I have run the fastqc to check the adapter sequences and I have found no hit for adapter so I am not trimming the adapter seq. and then after import pair end file to qiime2,
but fastqc report shows a large number of read with NNNNNN…what should I do with these noisy reads?
Overrepresented sequences Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 43433 30.947087911304916 No Hit CTTGGTCATTTATACACATCTCCGAGCCCACGAGACACTGAGCGATCTCG 14690 10.466988727858293 No Hit CTTGCGTTGAAGATGATGATGCCTATTAGCGGTGGCGGCGACGTGGCCGA 11563 8.238923802602141 No Hit
I have a look on demax.qzv file and I am thinking to use the below command?
demux.qzv (294.9 KB)
qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --o-table table.qza --o-representative-sequences rep-seqs.qza --p-trim-left-f 34 --p-trim-left-r 20 --p-trunc-len-f 0 --p-trunc-len-r 0 --verbose --output-dir dada2_result
I will be thankful for your help and time.