I've been working on RRBS data these days. Raw data were processed using Trim_galore tool, in order to remove adapter and low-quality reads. The clean data were mapped to the reference genome using the Bismark alignment tool with default parameters(--bowtie2 --directional). Final Alignment report is like this:
Sequence pairs analysed in total: 17109021 Number of paired-end alignments with a unique best hit: 10941462 Mapping efficiency: 64.0% Sequence pairs with no alignments under any condition: 3219358 Sequence pairs did not map uniquely: 2948201 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Total number of C's analysed: 539400501 Total methylated C's in CpG context: 28032910 Total methylated C's in CHG context: 2657563 Total methylated C's in CHH context: 5817321 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 90723174 Total unmethylated C's in CHG context: 147210060 Total unmethylated C's in CHH context: 264959473 Total unmethylated C's in Unknown context: 1 C methylated in CpG context: 23.6% C methylated in CHG context: 1.8% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 0.0%
Is the resualt ok ? I want to know wether the 64% mapping efficiency is ok for RRBS data and why. And why is it so low compared to other NGS ?
Thank you very much.