Illumina summary spreadsheet. What statistics for 4 reads mean

Dear community,

I have a general question, but I can't find answer for it. In the run summary from HiSeq 4000 150x2 run we have sections "Cycle status", "Run Summary", "Read 1", "Read 2", "Read 3", "Read 4". What do these Read 1-4 mean?

Thanks!

sequencing next-gen

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updated 6.1 years ago by GenoMax

• written 6.1 years ago by semion.leyn •

1 answer

Read 1 - Read 1/Forward reads
Read 2 - Index 1
Read 3 - Index 2 (dual indexed sample)
Read 4 - Read 2/Reverse reads

In Illumina sequencing, index reads are not part of the main sequencing. Cycle numbers you see in the summary report should indicate above structure.

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written 6.1 years ago by GenoMax

Thank you very much for such a quick answer!

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written 6.1 years ago by semion.leyn •

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