Dear all,
I am working with Targeted Bisulfite Sequencing, which is a bisulfite sequencing of an Exome Capture Seq. After running FastQC I ended with a lot of PCR duplicates. I was about to remove them when I read in Bismark's manual that these should not be removed for RRBS. After a bibliographic search I interpreted that RRBS is, as the name states, a reduced version of the whole genome bisulfite sequencing, reducing complexity to just CpGs close to promoters and first exomes within genes, which made also sense for me and my data (exome capture), but I didn't find any other explanation. However, I also found this entry in Biostars and I see now that maybe this should be take into account just when RRBS is based in the use of restriction enzymes during library preparation, and this is not certainly my case as exome capture is based on the use of biotinylated probes and capturing.
Should I then remove these PCR duplicates for my TB-Seq? Can be TB-Seq considered as RRBS, as both are reduced representation of bisulfite sequencing, or these are two different methods given the differences in library preparation?
Thank you very much for your help. Victor
