Hello there,
recently I performed a MiSeq run (v3 kit, standard flow cell) with 40 samples and faced some difficulties. First of all, we forgot to add the sample sheet before the run. We added it after the run had finished and data were analysed just fine.
But now I am looking at my data and got quite bad results. Overall the cluster density was low (390 K/mm2), we usually have cluster densities of ~800-1000 K/mm2. But the most puzzling problem is that the MiSeq seems to have difficulties with the indexing. In the Sequence Analysis Viewer in the tab "Indexing" no indices are present, so the MiSeq tells me that no reads were mapped to Index Id. However, when I perform sequence analysis, some samples can be analysed, even though most of the samples can not. The Illumina Tech Support told me, that some of my samples were not demultiplexed.
Do you have any idea what went wrong or if/how I can fix this problem? My hope is that the data is there but only has to be re-analysed somehow.
Best regards
Julia
recently I performed a MiSeq run (v3 kit, standard flow cell) with 40 samples and faced some difficulties. First of all, we forgot to add the sample sheet before the run. We added it after the run had finished and data were analysed just fine.
But now I am looking at my data and got quite bad results. Overall the cluster density was low (390 K/mm2), we usually have cluster densities of ~800-1000 K/mm2. But the most puzzling problem is that the MiSeq seems to have difficulties with the indexing. In the Sequence Analysis Viewer in the tab "Indexing" no indices are present, so the MiSeq tells me that no reads were mapped to Index Id. However, when I perform sequence analysis, some samples can be analysed, even though most of the samples can not. The Illumina Tech Support told me, that some of my samples were not demultiplexed.
Do you have any idea what went wrong or if/how I can fix this problem? My hope is that the data is there but only has to be re-analysed somehow.
Best regards
Julia
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