The MiSeq Reporter analysis software outputs a demultiplexing summary file called DemultiplexSummaryF1L1.txt that can be used to troubleshoot demultiplexing issues.
Where is the DemultiplexSummaryF1L1.txt file?
What information is in the DemultiplexSummaryF1L1.txt file?
Figure 1: The tile summary section shows the percentage of reads demultiplexed to each sample, per tile.
The second section of the DemultiplexSummaryF1L1.txt file (Figure 2) lists the 100 most common index sequences (whether assigned or undetermined) for Index Read 1 and Index Read 2, and the number of times each index was found. The list also shows the reverse complement of the index sequences found (for your reference only). In the DemutiplexSummaryF1L1.txt file, periods (...) in the index sequences represent positions where the base calling software on the MiSeq could not make a base call.
Figure 2: The most popular index sequences section of the DemultiplexSummaryF1L1.txt file lists the top 100 index 1 and index 2 sequences found.
When troubleshooting demultiplexing issues, the lists of index sequences can be used to compare the expected index sequences (those in the sample sheet) to those that were found.
Some common causes for poor demultiplexing that this list can reveal are: