when I use the dada2 of qiime2 to demux single-end .fastq file, I met an unexpected results of the .qzv file. There was nothing in the windows of interactive quality plot.
The codes were used as below:
(qiime2-2023.7) [XYB@Dulab PRJNA449268] qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path merge_files_PRJNA449268.tsv --output-path single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2
***Imported merge_files_PRJNA449268.tsv as SingleEndFastqManifestPhred33V2 to single-end-demux.qza***
(qiime2-2023.7) [XYB@Dulab PRJNA449268] qiime demux summarize --i-data single-end-demux.qza --o-visualization single-end-demux.qzv Saved Visualization to: single-end-demux.qzv
Do you mean that when you loaded the .qzv in the browser you only saw a blank page? What browser did you use? What happens if you put the same qzv in old-view.qiime2.org?
Thanks for your response！！I am sorry about the vague description. I mean when I load the qzv file to the new the website of qool tools view, I can't see anything in the quality of sequencing base....
It looks like this isn't a problem with the visualization, but with your sequences. They seem to not have recognized quality scores. Could you share a screenshot of a couple of the fastq sequences that you imported, and share the command that you used to import them?
Im not sure why those records have only ?s as quality scores. Are you sure that this file is one of the ones you imported? Because the ? character is a valid quality character that codes for the quality score 30 in your case.
I am sorry for my disappearance. I checked the downloaded files and I am sure this file is one of the ones I imported~ Since I cannot handle this issue, I finally dropped this dataset for my analysis. Thanks for your kindful help !
It was really the file imported into analysis. why all the fastq files have ? symbol in this project. It was so weird
