Hi there!
I have the fasta sequences for all my samples. I was wondering if it is possible to create an ASV table using fasta sequences? Can this be done in R?
Please could you let me know about the procedure.
Thank you.
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Hello Priyanka,
This discussion may be helpful, as this person also had sequences only (without quality scores, and fasta is just fastq without the quality scores): Deblur Plugin Set-up - #11 by jwdebelius
The best option is getting reads with quality scores if possible.
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Hi Colin,
Thank you very much. 
I now have the fastq files for my samples (50 fastq files for 50 samples). We did 16S rRNA gene sequencing on the PacBio platform. I'm not sure whether these files need to be demultiplexed before generating an ASV table.
Okay great!
Because you have one fastq file for each sample, this means they have already been demultiplexed.
You can import all those fastq files using the fastq manifest format. As described in that tutorial, there is a manifest.tsv file you can make that lists all these files.
Let us know if you have questions about making that manifest file!
Once the data is imported, you can denoise it into ASVs using this pipeline:
https://docs.qiime2.org/2024.5/plugins/available/dada2/denoise-ccs/
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Thank you! I'm so sorry for the late reply.
One more thing - Can fastq manifest format and denoising it into ASVs all be done using QIMME2 on Galaxy (https://usegalaxy.org/)?
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Yeah! Galaxy uses Qiime2 'under the hood' and it's all interoperable.
(Galaxy makes the same errors as the CLI, so you can still ask us questions here if you get stuck!)
I did a trial and uploaded 3 fastq files on galaxy. I couldn't find the fasta manifest format on the tools section. So I went to 'qiime2 tools import' which imports the data into artifacts and there was an error.
I am confused whether the data imported must be converted to artifacts first before go ahead with 'qiime 2 dada2 denoise ccs' and this part requires qza files.
Sorry for all the questions.
Hello Priyanka,
I can see the Fastq manifest formats using the qiime tools import Galaxy plugin.
But this still requires you to make the fastq manifest file and upload all of your fastq files.
I'm not an expert on using Galaxy, so perhaps another member of the team can answer it better than me.
Hi Colin,
Thanks for your help!
Hi there! 
I am trying to import demultiplexed sequence data onto Galaxy. According to the one of the tutorials, the fastq files must be uploaded as url links (as seen in the image below).
However, I don't have the links to the fastq files and I am unable to upload the data (as files) following the steps mentioned in the tutorial.
Is there a way to obtain the URL link from a fastq file?
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I'm not sure the best way to do this with Galaxy!
Let's see what other folks recommend. You could also post on Galaxy Forums (https://help.galaxyproject.org/).
Hi Colin,
Will do. Thanks!
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