Splitting fastq by sample using qiime1 mapping file in qiime2


I’ve got a single fastq file containing 16S RNA Illumina MiSeq V4 paired end sequences that I need to split by sample for a meta-analysis. The author of the paper provided me with a qiime mapping file that contains the sample ID, barcodes and linker primer sequences that would split the fastq file by sample in qiime1 using the split_sequence_file_on_sample_ids.py command. However, I am unable to install qiime1 on my server as it uses an older version of conda. Therefore, I want to use qiime2 to split the fastq file by sample instead but there doesn’t seem to be an equivalent command after looking through the tutorials. I’m a complete novice when it comes to qiime1/2 and I’ve looked on the forum but I can’t seem to find anyone else who has run into this specific problem.

Can anyone help?

Thanks in advance.

Welcome to the forum, @mimba30!

QIIME (1) is no longer supported - you're making the right choice by choosing QIIME 2 for your work. :slight_smile:

I don't have any experience with QIIME 1, but it sounds like you're trying to demultiplex your data. Take a look at the tutorials - they'll give you a good foundation. Specifically, I'd start with:

  • importing - this will help you get your data into QIIME 2
  • metadata - how QIIME 2 expects your metadata (mapping) to look
  • moving pictures - a high-level walkthrough of one possible single-end sequence analysis

Happy :qiime2:-ing!

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