how to importing data


I got the FastQ-formatted sequences that were sequenced in the PacBio platform using SMRTbell library. The seqs are demultiplexed. Because barcoded F and R primers amplified one fragment from entire region of interest (~1.0 kb), it does not seem to use the option combining two fragments amplified by F and R direction (R1 and R2) using a paired-end option. I found that the tutorials in qiime2 doc posted several choices showing how to import data for downstream analyses in qiime2 (e.g., Casava 1.8 single-end demultiplexed fastq). Do someone know which one is the choice to import my demultiplexed FastQ data for downstream analyses? If I could importing my data successfully, I think I can move to the next step "seq quality control" using DADA2 that I experienced before.




First of all, I'd like to warn you that your post violates a Code of Conduct - QIIME 2 Forum, your work is your work. Requesting someone's code is prohibited. Please, edit it accordingly.
Second, QIIME 2 does not have plugins for preprocessing PacBio data, but when you obtain a feature table can be you can use QIIME2 downstream with a plethora of analytical methods for tabulated data.


Thank you for pointing out this. I edited as recommended by you. Hee-Sung.

Hello @baehsung

I apologize, @lizgehret actually pointed out, that you can use q2-dada2 for preprocessing. But it only utilizes information from forward reads.
In case of paired-end sequencing I would look into official PB software: GitHub - PacificBiosciences/pbbioconda: PacBio Secondary Analysis Tools on Bioconda


Hi @baehsung and @crusher083,
I discussed this with some of the other QIME 2 Forum moderators, and we don't agree that this post constituted a code of conduct violation. Rather it seems that there was some a misunderstanding over what you were asking for. I apologize if this created any confusion.

I'm sitting next to @lizgehret right now and she has some additional information that she thinks may be helpful for you. She'll follow up with you on this post.

Hi @baehsung,

I wanted to share with you another forum post that provides an example of how you would import your PacBio reads (as you'll need to handle this step prior to dealing with the denoising/dereplicating of your data). Hope this helps - please let us know if you need any further assistance!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.