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My FASTQ files are bigger than 1.5 GB what should I do?

The free data analysis runs included with QuantSeq FWD/REV kits are limited to FASTQ files with a maximum size of 1.5 GB. If you have larger files you have two options:

Option 1

You can compress your FASTQ files and/or sub-sample the reads to reduce the size of your FASTQ files to 1.5 GB or less.

To compress the files:

  • For windows computers download 7-zip and re-zip with quality best.

  • For Mac OS and Linux this can be done with the command line command: gunzip -c some_file.fastq.gz | gzip -9 > some_higher_compressed_file.fastq.gz

To sub-sample reads:


Option 2

You can purchase data analysis codes for larger file sizes by contacting Here are the catalog numbers you need:

Catalog No.

Product Name


QuantSeq Data Analysis (FWD/FWD-UMI), 1 run, 0 – 3 GB


QuantSeq Data Analysis (FWD/FWD-UMI), 1 run, 0 – 6 GB


QuantSeq Data Analysis (REV), 1 run, 0 – 3 GB


QuantSeq Data Analysis (REV), 1 run, 0 – 6 GB

Please note there are different catalog numbers for FWD or REV runs as this controls the access to the specific analysis pipeline.

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