Arthur Rand
Arthur Rand
> For a single read that spans a site you can therefore change methylation call at that site in that read. Are you determining the methylation state of a position...
@mattloose let me know if you have additional questions.
Hello @billytcl, I wouldn't expect that you need a different threshold per read position. The intention of the threshold is to remove the low confidence calls from the analysis. All...
Hello @billytcl, Sorry for the delay, I was trying to get some example data for you - but I didn't quite get there yet. What I would expect is if...
Hello @billytcl, I've started to think about this idea in another context again, specifically short-reads and high depth. You could make a threshold at each pileup position that drops the...
Hello @hyunjokoo, Sorry for the slow reply. I'm going to answer your second question (visualization in IGV) first. I believe the latest version of the IGV desktop application will display...
@hyunjokoo let me know if you have any additional questions.
Hello @nextgenusfs That is correct. As noted in a [previous issue](https://github.com/nanoporetech/modkit/issues/19), the mixed delimiters are used so that the output is directly viewable with most commonly used genome viewers. In...
Hey @nextgenusfs, Probably the easiest thing to do is run `awk 'BEGIN{OFS="\t"} {NF=11; print} in.bed > out.bed'` then give that output to jbrowse2. The default output from `modkit` should conform...
@Ge0rges the default bedMethyl output _should_ be acceptable input to IGV. I'm using 2.15.2 locally and it works fine.