bismark_methylation_extractor

[zhangqc723]

Hi, I recently used the following command to extract methylation information for genome CpG sites from a BAM file. However, I noticed that some of the sites in the output are not actually CpG sites. As shown in the attached image (is ACA not CG), should I filter these out separately? Command: bismark_methylation_extractor
-s --comprehensive --parallel 12
--bedGraph --zero_based --cytosine_report
--genome_folder mm9
-o Lib_WGBS_mESC
XXX_sort.rmdup.bam_

Thanks for your help!