Thanks for bringing this up pmiguel. I saw this document a few days ago and was surprised to see that single amplicons got relatively good Q30 values and %PF. I'll be sure to ask our sequencing provider the cluster density and software version for our 3 failed HiSeq runs. Perhaps we are barking up the wrong tree and should consider alternative hypotheses.
One thing we just came to realise is that a non-optimal combination of indexes was used (AR001, AR002, AR003, AR004) rather than the Illumina-endorsed 4 plexes. I thought that should be added in case that could cause 0 clusters to pass filter during the index sequencing and/or data processing stages.
One thing we just came to realise is that a non-optimal combination of indexes was used (AR001, AR002, AR003, AR004) rather than the Illumina-endorsed 4 plexes. I thought that should be added in case that could cause 0 clusters to pass filter during the index sequencing and/or data processing stages.
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