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:
Check out this Subsampling a fastq file with awk a command line tutorial.
Option 2
You can purchase data analysis codes for larger file sizes by contacting sales@lexogen.com. Here are the catalog numbers you need:
Catalog No. | Product Name |
211.01 | QuantSeq Data Analysis (FWD/FWD-UMI), 1 run, 0 – 3 GB |
212.01 | QuantSeq Data Analysis (FWD/FWD-UMI), 1 run, 0 – 6 GB |
213.01 | QuantSeq Data Analysis (REV), 1 run, 0 – 3 GB |
214.01 | 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.