Entering edit mode
2.1 years ago
Thanh
•
0
I am aligning 2 paired-end fastq files (WES) to gh38 and writing the read group for the -R option. As I was reading this post about how to write the read group field suitable for using GATK in subsequent steps, I was wondering where I can find the information about the flow cell barcode and lane for the PU field. I've checked the paper and SRA for this information but can't seem to find it.
Look in the headers of your fastq files. If you are downloading this data from SRA and can't recreate the original Illumina fastq headers then you will need to make values up for those fields.