Can bisulfite conversion replace the Fragmentation Step in the xGen™ Methyl-Seq workflow?
It is not recommended.
Fragmentation solely by bisulfite conversion results in a broad size distribution of larger DNA fragments. Such fragments may be converted into library molecules. However, the wide distribution of library molecules will cluster poorly on the flow cell. If skipping fragmentation is unavoidable, we recommend examining the size of library molecules prior to library quantification, and, if necessary, performing a right-side size selection to remove very large library molecules to improve clustering on the flow cell.
This scenario will result in reduced complexity of sample representation.
Contact us for recommended modifications when relying on bisulfite treatment for fragmentation.