Figure 2. Data processing and analysis of m3C-seq sequencing reads.
Reads derived from non-bisulfite treated regular Hi-C sequencing are converted C to T (read1) and G to A (read2) in silico and aligned using BWA-meth, Bismark (bowtie1), and Bismark (bowtie1) followed by split-read alignment. Alignment of non-converted reads using conventional alignment pipeline is used as a standard (Conventional, Non-converted). For (a-d), the mapping algorithms were applied to a common test dataset (n=1) to make a fair comparison of their performance. (a) Percent of aligned reads as a pair. (b) Alignment accuracy of different alignment strategies compared with conventional Hi-C alignment using in silico converted reads. (c) Fraction of read pairs with cis short-range reads (cis < 1kb), cis long-range interactions (cis > 1kb), and trans interactions (trans) using different alignment strategies. (d) Similar to panel (c), but for 3C-seq (without conversion), bulk m3C-seq (with conversion, from the same sample as bulk 3C-seq), and combined 192 single-nucleus m3C-seq results. (e) Contact maps from chromosome 17 for conventional bulk Hi-C and bulk m3C data. (f) mC profiles near the Pou5f1 gene for conventional bulk MethylC-seq as well bulk m3C-seq. The experiment was repeated twice independently with similar results.