Importing Multiplexed Fastq Downloaded from SRA

I am attempting to import a fastq file that appears to have sequences for multiple samples (this is from a published study where they analyzed using QIIME1). While I have both reverse and forward fastq files from NCBI/SRA, I don’t have a barcodes file that i can use to demultiplex. The study provides a mapping file that looks like it was used in QIIME1 importing step, but is a tsv file that includes the headers sample, barcode sequence, linker primer sequence, reverse primer and some other descriptive metadata (see screenshot attached). Can this mapping file be used to demultiplex on QIIME2?


Hi @termofilos,
You can certainly use the cutadapt tool to demultiplex your fastq file by providing a metadata files that has the barcode sequences you found in the mapping file. You can see a tutorial on this here a well.

Hi @Mehrbod_Estaki, thanks for the prompt response. I’ll give that a shot and see how it goes. Thanks for the suggestion!!!

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Hi again @Mehrbod_Estaki, the method you suggested worked great. Thanks again!


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