Fig. 2

TRACE-RRBS Flowchart. The reference genome in fasta is first digitally digested into fragments mimicking a real RRBS experiment. These fragments are size selected, end repaired, A-tailed and an adapter annealed. They are further indexed using Bowtie 2. Both sequence reads and the reference fragments are converted fully from Cs to Ts for forward and Gs to As for reverse strand before alignment by Bowtie 2. After alignment TRACE-RRBS parses the bam, removes an adapter and incorporated Cs, and compares with unconverted sequence for methylation calculation