Qiime2 import fastq

[hongweiyin]

I am a new Qiime 2 user and I am attempting to import joined fastq files (this means that I have only one fastq per sample that includes R1+R2 joined).新建文本文档 (2).txt (1.3 KB)
This is my fastq file with BarcodeSequence and LinkerPrimerSequence,also i have a mapping flie liemapping.txt (510 Bytes)
ke
i am confused which do i choose for my data importing to qiime2 ,and also if i can use dada in the next analysis .
How can I import my FASTQ file?
Thank you very much

[thermokarst]

Hi @hongweiyin!

@hongweiyin

I am a new Qiime 2 user

Welcome!

@hongweiyin

I am attempting to import joined fastq files (this means that I have only one fastq per sample that includes R1+R2 joined)

Have you had a chance to review the "Analyzing paired end reads in QIIME 2" Community Tutorial? In particular, the section titled "Importing pre-joined reads" will get you started with importing your reads - then you can go back to the beginning of the tutorial and work your way through (skipping the "Joining reads" section, since you will have imported pre-joined reads at that point).

@hongweiyin

i can use dada in the next analysis

DADA2 works best with unjoined reads - DADA2's error model considers the forward and reverse reads separately, and joins the reads for you as part of the quality control step. If you want to work with ASVs, I would recommend working with q2-deblur (there are details on how to do that in the tutorial I linked to above).

Let us know if you get stuck or have any questions, thanks!