I am new to NGS first of all. I would like to sequence transposon flanking region, thus during PCR amplification step, instead of using primers supplied by Illumina TruSeq, I will use own customized primer (tailed with Illumina adapter sequence) which will bind specifically to the transposon end and start amplification. Lots of issue I need to settle for sample prep. But now my doubt is: during sequencing run, is it possible if we use own sequencing primer (in which I plan to design primer which binds to the transposon end region)? Say if I wanted to run on HiSeq2000. If I use standard sequencing primer, most of the first ~20bp of the reads will be the same (the transposon end) and how will this affect the coordination of clusters during first few cycles?
Sorry for the poor English used.
Sorry for the poor English used.
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