Importing Multiplexed Paired End sequences

hafizmtalha · September 21, 2019, 10:17am

I have 10 fastq files. 5 fwd,5 rev. and I excel file containing barcode sequence for fwd and reverse files. basically i have 50 gut samples from different regions. I want to import my data to qiime2. but i m unable to do it. If anyone could help me in this regard

Mehrbod_Estaki · September 21, 2019, 11:23pm

Hi @hafizmtalha,

Can you tell us what you have tried with regards to importing and what has failed for you? What were the errors?
This seems like a pretty simple paired-end multiplex impor process x 5 (once for each run)

hafizmtalha · September 23, 2019, 4:49am

I don't have barcodes.fastq file.

Mehrbod_Estaki · September 23, 2019, 7:36pm

Hi @hafizmtalha,

As long as the barcodes are in your sequences (and not in the headers of the .fastq files) you can use the cutadapt demux-paired plugin to demultiplex your reads using a metadata file. In your case the excel file. Give that a go and let us know if you run into any problems.