Importing 3 Casava 1.8 files

Hi! I am very new to Qiime2, and I have received 16S MiSeq data that I need to analyze. I received 3 files from the sequencing center - titled 5730-P1_S1_L001_I1_001, 5730-P1_S1_L001_R1_001 and 5730-P1_S1_L001_R2_001 so I assumed it is in Casava 1.8 format however I am still confused as to the files I got - I haven’t found topics on the forums showing how to correctly import using I1, R1 and R2.

I tried importing the R1 and R2 through Casava 1.8, viewed the quality plot, selected the trimming length and ran dada2, but I received an error message
An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.

I did it because I thought my data was already demultiplexed by the center but then I noticed that demux.qzv showed just 1 sample while there should be 45. Here is the quality plot. So this means that my data is multiplexed, right? Then how should I proceed?

Thank you and Merry Christmas!

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Hi @Tym!

Actually, it looks like you have multiplexed EMP-style reads (Casava 1.8 is a demultiplexed format):

https://docs.qiime2.org/2019.10/tutorials/importing/#emp-protocol-multiplexed-paired-end-fastq

Take a look at the link above and let us know how it goes!
:t_rex:

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Thank you! But how do I extract barcodes, forward and reverse reads from those files?

I just had a similar problem and followed the instructions on the protocol.

I found that I needed to rename the files first after gzip compression as follows: “forward” (for R1), “reverse” (R1) and “barcodes” (for I) with all of them having the fastq.gz extension.

After that import them as EMPPairedEndSequences and then demultiplex them.

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Thanks! I actually tried that but got an error for demultiplexing. And I also thought that R1 and R2 files contain both forward and reverse reads each just for two runs?

Please share the commands run (copy and paste), and the complete error observed (copy and paste when run with the --verbose flag).

Can you explain this question in a bit more detail? R1 and R2 are convention (usually) for forward (R1) and reverse (R2), but it isn’t a rule.

:qiime2:

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