Run Analysis and Data Collection
Upon completion of a run, the data is automatically sent through a series of custom pipelines. FASTQ files are generated for all samples within a run and provided to the user in Illumina 1.8x format. We perform quality control (QC) of the run using software provided by Illumina as well as FastQC to confirm that high quality data is provided.
Data is released to the user once it has passed our quality checks. All NextSeq and MiSeq run data are shared with the user via secure log-in SFTP site, where files are available for download for 30 days. Data from all NextSeq and MiSeq runs are stored for six months. After six months, all NGS runs are archived to tape. We strongly recommend that all users keep a back-up of all data provided by the Core.
NGS Run Guarantees
Each Illumina NGS platform delivers a maximum output dependent upon the type of flowcell and reagents used. In practice, this output can also be affected by the DNA source and the type of library created. It is our goal to have each run collect the highest quality and quantity of data possible for the set of samples being run.
The Genomics Core will guarantee a minimum of 80% of the maximum number of possible reads as listed by Illumina based on instrument type and reagents used if the Core completes all quality control (QC) on submitted total RNA and/or DNA and performs the library prep, final library QC, pooling and qPCR. All libraries used must pass QC in order for the run to be guaranteed.
The Genomics Core will guarantee a minimum of 70% of the maximum number of possible reads as listed by Illumina based on instrument type and reagents used if the user submits final library preps that use all standard Illumina reagents (ie: primers) and the Core completes final library QC, pooling and qPCR. All libraries used must pass QC in order for the run to be guaranteed.
It is our goal to have each run collect the highest quality and quantity of data possible for the set of samples being run, however at times there are limitations. The Core cannot guarantee a minimum data output in the following cases: when a run is performed using QC data provided by the user, if any custom sequencing/indexing primers are used in replacement of Illumina provided reagents, or a run that includes experimental libraries that have not been previously tested at our core or by Illumina.