How to convert .txt mapping file to barcode.fastq.gz

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Perfect! The index file is (or should be) your barcodes! :tada:

Here are some steps to hopefully get you moving in the right direction:

  1. Rename your forward reads to forward.fastq.gz and your reverse reads to reverse.fastq.gz
  2. gzip your barcodes $ gzip whatever-your-index-file-is-named.fastq
  3. Step 2 will create a new file, whatever-your-index-file-is-named.fastq.gz (note the "gz" at the end!)
  4. Rename that new file to barcodes.fastq.gz
  5. Follow along with the EMP Paired End Import Tutorial (skip downloading the test data).

You don't need to do anything with your mapping file in order to import these data, you should only need the three files referenced above (forward.fastq.gz, reverse.fastq.gz, barcodes.fastq.gz) in order to import your data. Where you will need to use the sample metadata file is when demultiplexing, but you shouldn't need to do anything special with that file, it should work for you as-is.

Please let us know if you get stuck! Good luck!!

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