Hi,
I am have trouble importing my paired end data into QIIME2 using 2023.9. I am not receiving any error messages but my demultiplexed sequence counts summary visualization is not correct. I am receiving multiple sequence summaries instead of a single mean/median/max/min (see image below).
I am importing paired end reads for each sample (for example, P001_S1_L001_R1_001.fastq.gz and P001_S1_L001_R2_001.fastq.gz) using:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path {metadata_p}/sample_manifest_2023.txt \
--output-path {step_1_p}/1a_paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2
followed by:
qiime demux summarize --i-data {step_1_p}/1a_paired-end-demux.qza --o-visualization {step_1_p}/1a_raw_data_quality.qzv
It appears that my paired end reads might not be lining up for each sample. I have checked my sample manifest and paths and sample ID are correct. But the output visualization is as follows.
Please let me know if you have any suggestions!