miseq undetermined fastq

[m_elena_bioinfo]

Good morning, I have a problem with miseq run.
I have generated 500Mb of Undetermined_sequence.fastq.gz and a sample in the trio was empty.
How can I determine raw index sequences in Undetermined file?
Thank you a lot

[kmcarr]

It sounds as if one of the indexes listed in your sample sheet was incorrect.

In the MiSeqAnalysis folder, under <run_directory>/Data/Intensities/BaseCalls/Alignment there should be a file named DemultiplexSummaryF1L1.txt. Among other things this file includes a table which lists each barcode (raw index) observed, its reverse complement and the count it was observed. Loot at that file to see if there is an index with a very high hit count that was not listed in your sample sheet; odds are this was the index truly used for that library.

Of course how do you rule out the possibility that the sample sheet was correct (i.e. the barcode used for the missing library was properly listed) but the wrong library was pooled for your run?

[m_elena_bioinfo]

GReat! You are right! I fix my problem, I have wrong the index sequences in the sample sheet. So now, I have to re-demultiplex the sequences with the right indexes. How can I do this?

[kmcarr]

GReat! You are right! I fix my problem, I have wrong the index sequences in the sample sheet. So now, I have to re-demultiplex the sequences with the right indexes. How can I do this?

Open MiSeq Reporter in your web browser.

Open the Analyses tab on the left side and select the run you want to work with.

Select the "Sample Sheet" tab at the top of the window. This will give you an Excel like view of the Sample Sheet for the run. Edit the information directly in your browser.

Click the "SAVE AND REQUE" button at the top-right. This will run a new analysis with the modified sample sheet.

[m_elena_bioinfo]

Thank you very much for your help! The program runs and I have generated the new fastq. The last question is: how can I know from MISEQ reporter when the requeue and the rerun of "data extraction" finishes?