sequences proceeding Illumina adapter

[devaypi1]

My question: If I have a a 24 nucleotide long sequence before the sequencing adapter would my DNA fragment still attach to the flow cells? Is there a specific cleavage step to remove sequences beyond the adapter before attachment to the flow cell? My additional question is: When multiplexing when does the cluster identification occur?
Thanx for any answer.
P

[pmiguel]

My question: If I have a a 24 nucleotide long sequence before the sequencing adapter would my DNA fragment still attach to the flow cells? Is there a specific cleavage step to remove sequences beyond the adapter before attachment to the flow cell? My additional question is: When multiplexing when does the cluster identification occur?
Thanx for any answer.
P

I can only speculate. Seems like they would still work since binding to the flowcell is a hybridization. As long as the sequence complementary to the flowcell oligo is there somewhere the flowcell oligo should still bind the DNA. There is no cleavage event, but the flowcell oligo is what is extended by the polymerase during clustering. So nothing 5' of the flowcell oligo would end up being amplified.
Multiplexing has no impact on cluster identification. All Illumina instruments identify clusters at some point early in the first read. Index reads are always the 2nd (and in the case of dual indexes, the third) read.

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Phillip