Import PE data, Barcode and the R package DADA2

[hongqx (hongqixuan)]

Hi,

I am a beginner for QIIME2. And I try to import my PE reads into QIIME2, but I gained error information.
My data do not depend on EMP. So I tried to use qiime tools import --type "SampleData[PairedEndSequencesWithQuality]" --input-path .mypath --output-path name.qza. But it can not work. I think the reason maybe is my files have separated into several files? Should I rename my files with the sequence information?
And the second question is how to get the barcode from my fastq files? I read the python script for QIIME, it still work? Besides, the tutorial barcodes file conclude the first line with barcode sequence and quality score in the files. If the file doesn’t contain quality scores or something, it can’t work?
The last one is about the R package dada2. I have analysed my data in R and work well. I just worry about the result is not objectives. I read the question about the difference between them. But I still don’t understand which one is better for my data. Could you talk more? Especially, for QIIME2 beginner. And how to choose?

Thank you so much!

[Nicholas_Bokulich]

Hi @hongqx,
Sounds like your data are not in EMP format, which is a multiplexed format (one forward sequence file + one barcode file + one reverse sequence file if you have paired-end reads).

Your sequences are already demultiplexed so you do not have (and do not need) a barcode file. Instead, use one of the manifest formats to import as described here.

Please ask your question about dada2 in a separate post to make that information more searchable by other forum users. I am not entirely sure what you are asking so please add more detail on the commands you are trying to use.

I hope that helps!

[hongqx (hongqixuan)]

Thank you so much. I change my file format as you said, it works well. And sorry to the dada2 question, I will ask in other posts. Anyway, Thanks.