Hi everyone, I'm a graduated student which study in epidemiology master program!
Since my thesis topic is related about depression and gut microbiome, I recently received some files that represent each stool DNA sequences, which are using Miseq and Miniseq tech.
But when I tried to import my data which from Miniseq tech, the system told me
So I checked the raw fastq.gz data from the biotechnology company. I found that each sample id had more than 1 forward/reverse read, my problem is how can I fixed this problem?
My recommendations would be to first, check with your advisor/sequencing center/biotech company and see how they ran your samples. My suspicion is that you have samples per true sample across multiple lanes. If this is the case, I’d recommend importing with the manifest format using a unique name for each sample/lane combo, processing. your data, and then using the group command to combine the multiple samples.
Hi @jwdebelius,
Appreciate for your replying!!
Yes, I’ve check the fastq file by using vim on the linux server, confirming that each forward/reverse file of each sample is different. I guess that each sample’s read was cut into 3~4 forward/reverse files.
Further, I also use manifest format to import my sequence data, but I’m wondering how to type my manifest context for each sample? And how to combine them?
What I meant was I try to import my data into QIIME2 by manifest file (txt file), but as I mentioned, my Miniseq data of each forward read had more than one files.
For instance, sample ID 618320 was one of my patient, the following files were the raw data of FORWARD read.
618320_S1_L001_R1_001.fastq.gz
618320_S1_L001_R1_002.fastq.gz
618320_S1_L001_R1_003.fastq.gz
So the problem is this patient’s sample have three files of forward read and reverse read, respectively.
And the following is my context of my import manifest file:
The error message says each sample must have a unique name - which is fine. I might try something like 618320-A. I would recommend the v2 manifest. Then, I think you should follow the advice from my last post:
