Hi everyone, I'm a new user of Hiseq, this is a first time that I'm running a multiplex run and I have some concerns about Index read. Until the index read, the quality values were very high but after they dropped dramatically (see attached screenshot). Does it mean that I will not be able to demultiplex my samples?
The multiplexing was done for one lane only (adapters 2, 4, 5, 6 and 12) and for all other lanes only one sample per lane was used. Can this be an issue? As far as I can conclude from this topic: http://seqanswers.com/forums/showthr...quality&page=2 this can also affect the quality of Read 2?
For library preparation I used TruSeq DNA Sample Prep Kit, if this matters.
The multiplexing was done for one lane only (adapters 2, 4, 5, 6 and 12) and for all other lanes only one sample per lane was used. Can this be an issue? As far as I can conclude from this topic: http://seqanswers.com/forums/showthr...quality&page=2 this can also affect the quality of Read 2?
For library preparation I used TruSeq DNA Sample Prep Kit, if this matters.
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