Rrbs Is It Different From Bisulfite Seq

Question

[Honey]

I was wondering in some papers RRBS is used is it same as bisulfite seq in other papers? What is the difference?

Thanks

Answer 1

[Devon Ryan]

RRBS is reduced representation bisulfite sequencing. So, it's BS-seq, just not of the whole genome (WGBS, or "whole-genome bisulfite sequencing"). This is typically done by predigesting the genome with a restriction enzyme (e.g. MspI) and then selecting a size-range of the resulting fragments for sequencing. RRBS gives higher coverage of target* areas at lower sequencing cost.

*"target" is perhaps the wrong word, you aren't really targeting a particular region of the genome, but rather enriching for a subset of the genome.

[Arindam Ghosh]

During analysis is it possible to detect if a given fastq file contains WGBS or RRBS data? One method would be to explore the SAM/BAM file using a genome browser. Any other specific things that can be used to differentiate?

[Charles Warden]

Maybe the alignment would be the most clear way to tell the difference (unless you had a highly fragemented and/or low input sample, and it wasn't immediately obvious if coverage was in CpG Islands for fragmented randomly across the genome).

However, before aligning RRBS reads, I would run Trim Galore!

https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

So, I think the trimming of due to the RRBS parameters should be different. Also, maybe FastQC can also identify features related to untrimmed RRBS reads?

[Charles Warden]

This is already a good answer, but I feel like I should also provide some links to get more detailed information:

https://en.wikipedia.org/wiki/Reduced_representation_bisulfite_sequencing

http://www.nature.com/nrg/journal/v11/n3/abs/nrg2732.html

Answer 2

[yupeng he]

Just want to add some to the already excellent answer by Devon.

Because the recognition sequence of MspI is CCGG, RRBS reads are extremely enriched in regions with high GC content. These regions are typically CG islands or promoter regions. Therefore, RRBS is a great way to get high coverage methylation data on promoters but it generally misses the intergenic regions (where around half of the enhancers are located). Although people used RRBS to study distal regions such as enhancers and distal transcription factor binding sites, only a tiny fraction of them can be covered and there is no guarantee that the covered ones are representative. Just be cautious about conclusions about distal regions drawn simply based on RRBS.