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Quality control of genomic resequencing data from a HiSeq gavin.oliver Genomic Resequencing 2 06-30-2013 01:48 AM
Short-read quality control software. desmo Bioinformatics 3 11-25-2011 12:06 AM

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Old 11-11-2014, 04:26 AM   #1
JGeskes
Junior Member
 
Location: Michigan

Join Date: Nov 2014
Posts: 1
Default HiSeq Control Software v 2.2.38

Hi there,

We recently installed the latest version of HCS on our HiSeqs. This was supposed to eliminate the need for control lanes and or phiX spike ins for low diversity samples. We ran a AT rich genome on the new software and had 69% PF. With the previous software this genome ran fine (95% PF). We also ran a SMARTer stranded pool that has low diversity in the first few cycles and the cluster density varies by as much as 200K clusters/mm2 between adjacent tiles. Has anyone else upgraded to the new software and had success or similar problems?
Thanks,
Jeanne
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Old 11-11-2014, 10:44 AM   #2
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,238
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With this software upgrade 10% Phix spike in for low deversity libraries is recomended.
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