[R] Microbiome 16S amplicon analysis in dada2

Jeff Newmiller jdnewm|| @end|ng |rom dcn@d@v|@@c@@u@
Sun Aug 21 00:10:23 CEST 2022

1) The Posting Guide warns you to use a search engine to familiarize yourself with the obvious answers before posting. "fastq file r" brought up quite a bunch of promising results. If those results are not useful, do expand on why they weren't when asking anyone for further help.

2) The Posting Guide also warns you that these mailing lists are plain text only ... you sent formatted text and automated systems including your own email program collaborated to strip the formatting. This frequently damages or removes information the sender thinks we will see... so figure out how to tell your email program to send plain text when posting so we won't be left in the dark about what you think is obvious.

3) There is usually more than one way to import files of any type... and the choice you make could be poorly matched to the size of your data or the type of analysis. Do ask this "best practice" question in the Bioconductor help area [1] where you can find many more experts in this specialized use of R than here. Try to be a bit more complete in your question so they can offer informed answers relevant to the size and scope of your analysis.

[1] https://bioconductor.org/help/

On August 20, 2022 2:13:20 PM PDT, Anas Jamshed <anasjamshed1994 using gmail.com> wrote:
>I've 80 FASTQ files ( 40F and 40R) for C57BL6 mice microbiome sequencing in
>80 different folders and all are paired-end. How can I upload all of them
>in R for dada2 analysis?
>	[[alternative HTML version deleted]]
>R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

Sent from my phone. Please excuse my brevity.

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