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Old 11-24-2015, 01:33 PM   #6
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,238
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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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