How to understand the reads of mapped to the minus chain (Crick Chain) in Bisulfite-seq would be such reads ?
I do understand C->T change for the reads which mapped to positive/forward chain, However, I do not understand why the reads mapped to minus/reverse chains are same with the positive reference chain, except G->A change.
How does it works for bisulfite squencing?
"The reads in forward chain displayed as it original sequence while the reads in reverse chain were reverse complementary displayed. I do know why they are use different principle to display such two kinds of reads and how to distinguish these two kinds of reads before alignment?"
As to Figure 1c, do you know how to show raw reference and bisulfite treated reference together?
Figure 1a, 1b: These two figure are the same example with different mode at samtools tview:
Eventually, I think it know what happened here. Thanks all the same for your helps.
As the strand identity of a bisulfite read is a priori unknown, our bisulfite mapping tool Bismark aims to find a unique alignment by running four alignment processes simultaneously. First, bisulfite reads are transformed into a C-to-T and G-to-A version (equivalent to a C-to-T conversion on the reverse strand). Then, each of them is aligned to equivalently pre-converted forms of the reference genome using four parallel instances of the short read aligner Bowtie (Fig. 1A). This read mapping enables Bismark to uniquely determine the strand origin of a bisulfite read. Consequently, Bismark can handle BS-Seq data from both directional and nondirectional libraries. Since residual cytosines in the sequencing read are converted in silico into a fully bisulfite-converted form before the alignment takes place, mapping performed in this manner handles partial methylation accurately and in an unbiased manner.