BSseq method clarification

  • determined the following during conference call:
    • samples were digested with MspI but not size selected prior to library prep
    • digested genomic DNA was randomly primed during first round of PCR in library kit (see kit schematic)
      • all read start sites should be now be random and no longer at the MspI cut site
      • we DO want to deduplicate because we do not expect reads to stack up since they are randomly primed
    • we should follow bismark user guide recommendations for TruSeq DNA-Methylatin Kit for trimming
      • trim an extra 8bp off both ends of reads

New Trimming Pilot

New Trimming on all data

Alignments on newly trimmed data