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What to do if the read group information is not properly available?
There are recommendations how to work with read groups (https://gatkforums.broadinstitute.org/gatk/discussion/6472/read-groups)
However, I was wondering how to proceed if the read group information is not properly available - so when I am working with public data. SRA strips/replaces the read names from the fastq files so I basically only have a run, experiment and biosample ID from SRA. I am aware that working with public data is always difficult but I am trying to find the best possible way to handle this.
Thanks for your input!