Hi, I'm quite new in bioinformatics and working with paired-end FASTQ files (*.fastq.gz) that I think already demultiplexed by the sequencing facility.
I have imported these files by using manifest file and ran demux summarize to check the quality by using below commands:
qiime tools import
(Another quick question here, I used tried to use Phred33v2 with tsv file, but it gave an error message as below:
Traceback (most recent call last): File "/home/cbjeong/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/util.py", line 90, in parse_format format_record = pm.formats[format_str] KeyError: 'PairedEndFastqManifestPhred33v2' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/cbjeong/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data artifact = qiime2.sdk.Artifact.import_data(type, input_path, File "/home/cbjeong/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/result.py", line 206, in import_data view_type = qiime2.sdk.parse_format(view_type) File "/home/cbjeong/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/util.py", line 92, in parse_format raise TypeError("No format: %s" % format_str) TypeError: No format: PairedEndFastqManifestPhred33v2 An unexpected error has occurred: No format: PairedEndFastqManifestPhred33v2 See above for debug info.
qiime demux summarize
These are the quality plots:
The Q score is dropping so rapidly which seems unusual, so I ran Dada2 in R.
And Q scores for foward reads of my seven samples were as below:
For me, the results from Dada2 in R looks more reliable.
I am not sure what I did wrong in Qiime2.
And is it correct to obtain only two representative plots for forward and reverse reads even though I imported 14 FASTQ files?
Any comments or advise would be highly appreciated!