Displaying Run Information
iSkyLIMS will provide different information about the run in separate "panels box".
The first panel will show information about the run, like:
- State of the run
- Dates
- Disk space used
As you can see there are quite some information about the dates. These are the dates for the main steps from the run is recorded in iSkyLIMS until the run is completed. The explanation of each dates are:
- Run was recorded on date. Is the date when Wetlab Manager create the Run in iSkyLIMS.
- Run date. Is the date when the run start in the sequencer.
- Run Completion Date. Is the date when the sequencer machine finish the sequence.
- Bcl2Fastq finish Date. Is the date when the finish the Bcl2fastq.
- Run finish Date. Is the date when iSkyLIMS finish to handle the Bcl2fastq files and finish the disk space usage. Is at this time when run is set to Completed
One of the important facts for a run is to compare, at the first glance, the quality of your run vs others.
To do it we have created a graphic with the most relevant quality information ("Q >30", "Mean Quality Score", "Yield MB" and "Cluser PF").
The run is compared with the runs that have been create on the same year. This is done on propose having in mind that processes in the laboratory are normally improved to have better quality. Then the run has to be compared with the ones that have similar quality procedures.
IMPORTANT. The values in the graphic above are normalized, in order to display on the same graphic values that are quite different.
Last part of this basic information is to show the associated projects to the run as well as parameters used during sequencing.
By default the table with the used Run parameters is collapsed. Click on the "+" to display the full parameter list.
The associated projects panel displays the projects that are part of the run. You can click on the project name. You will be redirected to display the project information.
Next piece of run information is to display the flow cell summary (combining all projects in the run), to check the overall quality of the run.
The first information that we can see is the number of the samples in the run, the Cluster (Filtered and Raw) and the Yield.
We can also see the percentage that each project represent in the total of the run.
Note.
The "Unable to identify the project" are the set of samples that could not be assigned to any projects because the index found while sequencing did not match with the ones defined in the sample sheet.
The summary information, described above, is split by lane to identify if there was any problem in any of the lanes.
As mention before the index that could not be matched to any defined in the sample sheet, it is named as "default project", where all the information are grouped and showed in the following picture.
Note that in this case the Number of the Samples is "1", because of the grouping mention before.
Also this information is split into lanes to identify possibles issues an a specific lane.
The Unknown Barcodes are the one mention above as "default project" but now we are looking more in detail to check the coded bases for each one to identify them. Only the top 10 per lane are presented in the table.
Note that a big number of these "Unknown Barcodes" can be impacted in the next phases of the bio-informatics analysis.
To check easier the most frequents unknown barcodes a pie graphic is showed. The graphic displays the sum of all unknown barcode described in the previous table.
The table besides the graphic is trying to match the unknown barcode with the barcodes defined in the index library kit. This will be used to decided if there was an error when defining the index in the sample sheet, because a library was set by error.
Finally, at the bottom there is a panel with 3 tabs containing “run metrics”, “lane metrics” and “charts”:
Click on each tab to see the quality information in the Run, and on charts tab to see the "Data By Lane", "Flow Cell", "Data by Cycle", "QScore Heatmap", "QScore Distribution", and "Indexing QC".
IMPORTANT.
The Run information described is displayed according the information is available during the life cycle of the run. Here is explained the information when the Run is Completed.