View Single Post
Old 11-17-2011, 11:23 AM   #1
Junior Member
Location: East Coast US

Join Date: Jun 2010
Posts: 8
Default Sequencing a Low diversity library on the HiSeq

I am preparing a custom multiplexed library that will fall into the "low diversity" category. Low diversity meaning the first 5 nucleotides of read 1 will be identical among all clusters. There is a well known and well documented problem with cluster identification for low diversity libraries (outlined here: ).

The above paper and many of the comments on these forums refer specifically to the GAII, and suggest that spiking the library with 40-50% phiX control resolves the cluster calling issue.

Now that the GAIIx has been all but phased out, I need to run my low diversity library on the HiSeq. The problem is that I don't know of anyone that has successfully run a low diversity library on a HiSeq, and my core informed me today that they have tried several times to run low diversity libraries but got awful results on the HiSeq, even after spiking with phiX %50.

My question is, has anyone had success running low a diversity library on the HiSeq? If so, how did you manage to get it to work. Because my study does not require a massive number of reads, I am considering spiking my sample with up to 90-95% gDNA, hopefully drastically increasing the diversity and resolving cluster identification problems. Does anyone have experience running low diversity libraries on the HiSeq that could give me some advice?

Thanks so much!
Simcom is offline   Reply With Quote