Hi everybody,
We are doing MeDIP-Seq. After denaturing and enriching our DNA we are currently using the Accel-NGS 1S kit to make Illumina sequencing libraries from the resultant single stranded methylated DNA.
When we used the Ion Torrent version of the kit, everything worked perfectly, however, we appear to be having sequencing problems with the Illumina version. Despite loading 12pmol (Kappa Quantified) on a MiSeq we have a low cluster density, but more importantly, we have only 30% of the clusters passing QC.
There is something in the Illumina kit, or the actual sequencing that we don't have under control.
Has anybody successfully used this kit with an Illumina MiSeq???
Thanks
Jon
Did you use KAPPA quantification kit designed for Illumina? You should also look in to the "images" in MiseqOutput folder, maybe you have overclustering, if so try loading less library....
We are doing a repeat run at this very moment. This time we loaded less library on, as Illumina thought it was either a chip problem, or overclustering that we had, rather than a library problem.
Our repeat looks good so far, suggesting that it was a chip problem.
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