René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"feature to use read from bam files in igv before bisulfate conversion state","articleBody":"hello. \nI just wanted to ask if there is a feature to convert the alignments after the use of abismal, such that i can use igv for visualization of the bam file? because if i do it now, I still have Cs converted when there was no methylation present. and then it looks like everywhere are errors when mapping. also the mapping quality score is currently not valid or usable (always 255). \nOriginally, I just wanted to compare 6 samples aligned with abismal vs bismark to figure out why bismark in combination with methylkit is able to detect some methylation sites in a promoter, however, abismal in combination with methylkit only detected these sites only in three out of six of those samples for some sites, some sites were not captured at all and some sites only in two animals. so i wanted to go back to the alignment and see if it was an alignment discrepancy between abismal and bismark and not enough reads capture those sites. eventually i want to figure out at which step the abismal-methylkit pipeline lost those methylation sites in some samples. \nlooking at bedgraph files from bismark and converting the methylation info file from abismal to cov or bedgraph showed that methylation sites were already missing at that point, although coverage is always higher with abismal. especially after using \"sym\" in the dnmtoolbox. \n\ncheers\nTom","author":{"url":"https://github.com/chuddy-ibk","@type":"Person","name":"chuddy-ibk"},"datePublished":"2025-02-27T14:15:38.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":2},"url":"https://github.com/258/dnmtools/issues/258"}