How to demultiplex 16S PE Miseq reads?

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7.7 years ago

Lina F ▴ 200

Hi all,

I received four files from the sequencing center with a recent 16S Miseq run:

R1, R2, I1 (all fastq.gz), and a Qiime-type mapping file (with barcodes in it)

I want to demultiplex these files so that I get one R1 and one R2 fastq file for each sample in the end.

However, I'm not sure how to proceed. Most workflows online seem to want to merge the reads, but I'd like to keep them separate.

The lab tech mentioned that the barcodes in the mapping file correspond to the data in the I1 index file somehow, but I'm not sure how exactly these match up.

If anyone knows of a tool that does this, or can suggest a general pseudocode algorithm that I could code up, I'd appreciate it!

Cheers,

~Lina

miseq demultiplex fastq 16S paired end reads • 4.1k views

ADD COMMENT • link 7.7 years ago by Lina F ▴ 200

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Seen this? http://qiime.org/tutorials/processing_illumina_data.html This looks like it explains how to work with Qiime mapping stuff and demultiplexing.

ADD REPLY • link 7.7 years ago by WouterDeCoster 47k

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It would be simple for the core that ran your samples to demultiplex this data. At least ask to see if they would do it.

ADD REPLY • link 7.7 years ago by GenoMax 141k

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