Hello,
I have a raw data demultiplexed and still with adapters and I would like to visualize the interactive quality plot of the demultiplexed sequences. However, running the tutorial, after demultiplexing I have a file called demux.qzv where I can visualize the interactive quality plot. Since I do not need to do the demultiplexing step I don not generate the demux.gzv file. Therefore, how can I see the interactive quality plot of my demultiplexed paired end raw data? which plug in shall I use? I only have 2 fasq.gz files (forward and reverse) from ilumina
Welcome back to the forum!
You can use your imported sequences directly in the same command from the tutorial to create quality plots. Also, you can use cutadapt to remove primers first and then visualize output before denoising
Cant understand well. I need to import first the data to qiime2 so i can generate demux.gzv fle to visualize the interactive plot., dont I?
Also, I want to import the data with Casava 1.8 paired-end demultiplexed fastq but also
I found that when you run the command
wget
-O "casava-18-paired-end-demultiplexed.zip"
"https://data.qiime2.org/2021.11/tutorials/importing/casava-18-paired-end-demultiplexed.zip"
Resolving data.qiime2.org (data.qiime2.org)... failed: Name or service not known.
wget: unable to resolve host address ‘data.qiime2.org’
Could you check this please too.
Yes, you need to import your demultiplexed reads into Qiime2 format in order to visualize it.
If you have your own data you should import it to Qiime2. With this command you are trying to download example dataset from Qiime2.
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