.txt to .fastq.gz file for barcodes from Ion Torrent Sequencing


Like Christina DeVera (Aug 17), I am trying to convert a .txt file to a fastq.gz file for my barcodes for analysis in QIIME2. However, unlike her, I do not have an index file, only a single 1) fastq file (sDMDMm2.fastq.gz) and 2) txt file (sDMDMm2_map.txt) for barcodes. You can see both files at: https://figshare.com/articles/16S_rRNA_amplicon_data_from_the_paper_The_outer_mucus_layer_hosts_a_distinct_intestinal_microbial_niche_/1499145

How may I convert the sDMDMm2_map.txt file to a fastq.gz file? Or do I need to analyze it another way?

Many thanks for your help!

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Welcome to the forum @Noah1 !

I recommend getting in touch with the authors of that data to understand where the barcodes are in the fastq files and if they have recommendations on how these data need to be prepared for analysis in QIIME 2. The txt file is just a sample metadata file that lists which barcodes correspond to each sample, but are not the barcode reads themselves.

The barcodes are probably included at the 5’ ends of the sequences in the fastq file, in which case you can follow the q2-cutadapt tutorial to import and demultiplex these reads.

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