Test cases

Example of a wrong index

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)