Is therer any suggestions on mapping rate of WGBS data?

Question

[Zeng Jingyu]

Hi everyone,

I'm recently working on a batch of WGBS data, we are evaluating the sequencing outcome.

We used BitMapperBS to align the reads, but the mapping rate of our samples varies in different samples from ~65% to ~75%.

I wonder if there's any standard in WGBS mapping rate? It's my first time working on WGBS data and the mapping rate is obviously too low compared to the WGS data I used to handle. We need some criteria to filter the samples and understand the sequence qualities.

By the way, the average sequencing depth is ~30X.

Answer 1

[Papyrus]

Mapping rate for bisulfite data is typically worse because of reduced complexity of the sequences. The efficiency will depend on your read length though, also on the species being mapped, aligner used, etc. In my personal experience mapping rates from 65-75% (using Bismark) in mouse/human are often observed for samples with decent/good quality.

[Zeng Jingyu]

Thank you for your answer!