bcl2fastq problems with the yield

Question

[Margo]

Dear people, I am currently trying to demultiplex the raw data files I got from NovaSeq with bcl2fastq tool. Well, the code seems to work right as I am getting the output, the problem is that the index mismatch rate is 99 to 100, and hence, I am not getting any yield. I believe I am missing some kind of a detail, but can't figure out what specifically.

These are the headers I have in the SampleSheet:

[Data]                              
FCID    Lane    Sample_ID   P7_INDEX_ID Index   Index2  Recipe  Control Sample_project

Will be very gratefull for our suggestions!

Answer 1

[swbarnes2]

The simplest answer is you were given the wrong indices. There is a report which says what indices you did get, or you can use a bit of grep to find out what the most common indices in your undetermined file is. Compare those with what you put in your sample sheet.

Also, it always helps when asking a technical question about software to include the command line you used to run the software, though if bcl2fastq ran to its end, your command line is probably okay.

[Margo]

Thank ou for reply! I am now wondering how the indexis can be wrong? Do you mean I did not use the right version of them? Because I am sure I provide them correclly.. index1 is i7 and index 2 is the reverse compliment i5. Here is a part of the summary:

[GenoMax]

index1 is i7 and index 2 is the reverse compliment i5.

If you have dual indexes you are showing the summary of just one index.

There are some samplesheet examples in this thread that you may want to check.

[swbarnes2]

We already understood that the indices you were expecting were not there. Don't you think it would be more useful to examine the barcodes that were found?