CZI-CABANA Workshop discussion thread

Same for me, the YouTube link is showing as restricted today when yesterday I was able to view it just fine.

Maybe you try searching “QIIME 2” on YouTube

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The video is now working but the audio is shut down, can you guys listen to it?

Thanks for this chance!

yes i can listen to it, very smoothly

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Hello @chiara ! I am currently listening to the youtube stream and there is audio. I would suggest checking your personal set up. Hope this helps!

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To add to the discussion about raw sequences and what is inside;

I think you can check the length of the sequences to see if it is longer than the expected size. Let’s say read length is 2x250. Then, if we have sequences longer than 250 bp, doesn’t it mean that there are barcodes or index or something else?

Also, an option out of Q2, FastQC should show if there are Illumina barcodes in fastq files if I’m remembering correctly.

Lastly, yes, there is not a specific way to tell what is inside our files if it is not delivered with right info.

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Hi @the_dummy,

I agree on fastqc. To answer your question, not necessarily. It may depend on the prep kit and where are sequencing adapters. In my experience, the length of 250 bp includes everything, sequencing adapters (depending on kit ), barcodes as well as PCR primers and low-quality tails. Hence, for me when I saw 250 bp it means these are as raw as possible (for a 2x250 bp MiSeq run at least)



5 posts were split to a new topic: Why not use 100% database identity?

A post was split to a new topic: high chimera rate in dada2

Hi @llenzi,

In that case, I’m mistaken to rely only on my experiences.

Thank you very much!

4 posts were split to a new topic: sequence length variation after dada2

A post was split to a new topic: Fragment insertion tree error

A post was split to a new topic: Tools for alignments

A post was split to a new topic: Measuring representation in a fragment insertion tree

A post was split to a new topic: Databases for mouse and intestinal studies

A post was split to a new topic: How does DADA2 handle the sequence with different truncation lengths?

A post was split to a new topic: How to decide when to cluster after denoising?


A general, gentle reminder that this thread is not actively monitored during the workshop and you will probably have more success getting your technical and general questions answered if you post it in a unique thread.
I encourage you to use “General Discussion” for theory, “User Support” for specific issues, and “Technical Support” for bugs.

Thanks for your interest and participation!


Warm greetings!
Thank you for your response and suggestion. I will keep that in mind next time I post a question. Am curiously waiting for some answers too.
That was very helpful.
Thank you very much.
My sincere regards.