Arthur Rand

Hello @ziphra, If you randomly subsample the CRAM (`samtools view --output-fmt cram -h --subsample FRAC`) does it work? If not, could you send me that one?

Hello @ziphra, In my experience piping an HTS-file through `samtools` as you've done has the effect of cleaning it up - so I guess I'm not too surprised. I'm not...

Hello @Ge0rges, I've been meaning to do this, thanks for the poke.

@kylepalos Thanks for this! > When analyzing the outputs with balanced replicates, would you recommend always analyzing the balanced effect sizes and p-values (rather than the un-balanced/raw values)? The effect...

@kylepalos, In the comparison of the balanced vs "raw" MAP-based p-values. I think the off-diagonal points could be due to high apparent within-condition variance. I bet in most cases this...

Hello @richardheery, If you use the `--ignore-index` flag the reads in the output should be in the same order as the input modBAM - but this routine doesn't leverage as...

Hello @eesiribloom, Just a sanity check, are these plots generated from similar samples (and similar alignments). What are you looking for in terms of a mitigation strategy? The R10 models...

Hello @eesiribloom, Sorry about the delay in responding, I've been OOO. > Curious to know what you might recommend in this situation - maybe just sticking with default is best?...

Hello @eesiribloom, > I was actually wondering, if a site has allele-specific methylation would the probability come out as ~0.5 ? if so these sites would be filtered out automatically...

Hello @ekushele, Using secondary, supplementary, and duplicate alignments in `adjust-mods` is supported as long as the alignments have valid `MN` tags. These tags are required to properly evaluate the modified...