CZI-CABANA Workshop discussion thread

User Support
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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)

Cheers

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

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

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Hi @llenzi,

In that case, Iā€™m mistaken to rely only on my experiences.

Thank you very much!

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

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

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

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

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

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

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

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Friends,

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 ā€œGeneral Discussionā€ for theory, ā€œUser Supportā€ for specific issues, and ā€œTechnical Supportā€ for bugs.

Thanks for your interest and participation!

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187

Hi,
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.

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