I am am stuck with a problem. I am using dada2 for denoising of paired end Illumina reads of read length 150 bases each (both R1 and R2). The quality of the reads are good and consistent throughout the read length.
My first issue is as below:
When i am importing the reads all of the reads are getting imported. But when i am trying to vizualize the data post conversion, the quality column remains blank. However when i export the csv file the files have some quality scores.
My Second Issue is mentioned below;
I am using dada2 for denoising the reads I am only getting 90 reads post denoising. I am not able to understand why this is happening. It is very urgent for me to resolve.
I hereby paste the command that i used for denoising the reads. Please take a look
[The reads have Phred 33 encoding:]
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trim-left-f 1 --p-trim-left-r 1 --p-trunc-len-f 150 --p-trunc-len-r 150 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 14
Please help me in sorting this issue as soon as possible. I thank you in advance.