As of release 17.09, fastq data will have the datatype fastqsanger auto-detected when that quality score scaling is detected and “autodetect” is used within the Upload tool. Compressed fastq data will be converted to uncompressed in the history.
To preserve fastq compression, directly assign the appropriate datatype (eg: fastqsanger.gz).
If the data is close to or over 2 GB in size, be sure to use FTP.
If the data was already loaded as fastq.gz, don’t worry! Just test the data for correct format (as needed) and assign the metadata type.