The Local Run Manager 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.
Figure 2: The most popular index sequences section of the DemultiplexSummaryF1L1.txt file lists the top 100 index 1 and index 2 sequences found.
The third section of the DemultiplexSummaryF1L1.txt file (Figure 3) lists the 200 most common index pairs found (for dual-indexed runs).
Figure 3: The most popular index pairs section lists the top 200 most common index 1 and index 2 pairs found.
The index lists also contain a column that shows the reverse complement of the index sequences found (for your reference only). In the DemultiplexSummaryF1L1.txt file, periods (...) in the index sequences represent positions where the base calling software on the MiniSeq could not make a base call.
Some common causes for poor demultiplexing that the index lists can reveal are: