Test cases
Demultiplexing is done thanks to information stored in a SampleSheet file. In this file, the [Data] section contains sample names together with the index used.
Sample_ID,Sample_Name,Description,index,I7_Index_ID,Sample_Project
412,412,,TGACCG,TGACCG,
LMD666,LMD666,,CATTTT,CATTTT,
TaoP3,TaoP3,,ACAGTG,ACAGTG,
TaoP10,TaoP10,,GTGAAA,GTGAAA,
| Undetermined indices | Reads per sample (and undetermined) |
|---|---|
The plot in the left-hand side gives you the indices that are over-represented in the undetermined file. Those are the reads with indices that do not correspond to those provided in the samplesheet. Here, there is an index TGACCA that is found in large proportion. Looking at the plot in the right-hand side, we see that sample 412 is empty. The index for this sample is incorrect. If we correct the sample sheet, we should now see something as below. There are still some undetermined reads but the proportion is reasonably low.
| Undetermined indices | Reads per sample (and undetermined) |
|---|---|
In this set of plots, the first one shows a possible faulty lane. The FastQC in the middle plot looks fine. It is not amazing but not bad either. However, if we run the pipeline without merging, and redo the QC, we can clearly see the poor quality of the lane 2
| Undetermined diagnostic plot | QC with merging | QC without merging |
|---|---|---|
(Note: this was project B5055°