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Old 11-24-2015, 02:33 PM   #6
Jafar Jabbari
Location: Melbourne

Join Date: Jan 2013
Posts: 1,238

Once a cluster passes filter in R1, indexing read(s) and R2 will collect data for that cluster even if it physically is not present. There should be still sequence data for those low quality R2s and it should not be a blank sequence file.
Possible reasons:
1- Overclustering or close to the max density specially with large amplicons
2- Low diversity regions in R2
3- Issues with sequencing primers or reagents
4- Issues with instrument hardware

Time to call Illumina tech support.
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