I am trying quality-filter paired end illumina reads.
The paired-end-demux.qzv was obtained using,

qiime tools import 
--type 'SampleData[PairedEndSequencesWithQuality]'  
--input-path manifest.txt 
--output-path paired-end-demux.qza 
--input-format PairedEndFastqManifestPhred33

qiime demux summarize 
--i-data paired-end-demux.qza 
--o-visualization paired-end-demux1.qzv

I have used this code many times. However, this time I found that all the reads are the same in the demultiplexed sequence counts summary. Please see the attached picture

I think this is a strange result, but I do not know what the problem is.
Thank you very much for your help.

Hello @beilinzyd,

Welcome to the forums! :qiime2:

Yes, that result is strange! Looks like your reads are very short... and also all come from the same sample!

I'm not certain what happened, so here's my best guess: something got swapped in the manifest file or in your fastq files. Maybe a sample_I1_001.fastq.gz file full of barcodes was imported, which would explain the very short read lengths.

Have you already solved this problem? If not, would you be willing to post the first few lines of your manifest.txt file and also the first few lines of the .fastq files listed within? Let's see if we can solve this mystery!

:man_technologist: :woman_technologist: :face_with_monocle:

PS. Thanks for being patient while folks are busy over the holiday break. :gift:


Thank you very much for your help.
I still do not know what the problem is. I think the files I received might be not the sequence results. I have contacted the company, and I am still waiting for the reply.

Thanks again and enjoy your holidays.

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