feature to use read from bam files in igv before bisulfate conversion state

[chuddy-ibk]

hello.
I 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).
Originally, 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.
looking 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.

cheers
Tom

[chuddy-ibk]

here some screenshots from igv after preparation of the bam files comparing abismal after alignment with abismal after the uniq step and bismark bam files.
inerestingly, the "noise" in the bam files is the fewest in the bismark alignment, followed by abismal bam after uniq and lastly abismal bam directly after alignment. why could that be?
anyway, that specific site i show in the snippets below has coverage according to the abismal bam file, even though the coverage file does not show any counts for some samples in the meth file. any hint on why dnmtools-counts doesn't find those reads in the bam files?

cov files converted to bedgraph of all samples, which aligner used is indicated. meth file from dnmtools was converted to cov file first and then total read count was used for bedgraph:

bam of bismark and abismal after uniq of mut_3 sample:

bam of abismal top after alignment of mut_3 and bottom after uniq of mut_1 (which should have no coverage according to meth file:

[andrewdavidsmith]

@chuddy-ibk Very sorry but I might not have noticed your issue until now -- a couple months late. I'll try to find some time to look into it soon.