Anand Mayakonda
Anand Mayakonda
Hi, I have some naive questions. 1. In biscuit align setting `-b 1` aligns read1 and read2 to both strands. Is this the one recommended for non directional libraries ?...
I aligned my Nome-seq reads with bwa-meth. Now I want to look at ndr and endogenous methylation. Following your protocol, I need to generate vcf. Does the bam file and...
Hello Developers, I am following the short tutorial from [here](https://gnomad.broadinstitute.org/news/2021-09-using-the-gnomad-ancestry-principal-components-analysis-loadings-and-random-forest-classifier-on-your-dataset/) for ancestry classification. It was working fine when I had earlier versions of the gnomad and hail. I did a...
Hi Simon, I am trying to parse json files generated by map command but it seems that the `Uniqueness Reads` information is missing from it. However, they are reported in...
It shouldn't be hard to generate an [IGV browser session](https://github.com/igvteam/igv.js/wiki/Wig-Track) for bigWig files. It would be a nice addition to the existing functionalities. With `browser.toSVG()` command I belive it should...
Hi, Thanks for the tool. Could you please consider supporing [strobealign](https://github.com/ksahlin/strobealign) as a mapper option. It has both the aligner and mapping functions - similar to minimap2 - and can...
### Discussed in https://github.com/PoisonAlien/maftools/discussions/1051 Originally posted by **juferban** September 21, 2024 Hi, I tried to add clinicalFeatures to my oncoplot that are continuous variables. While I manage to do it,...
Hi @tkik We should think of supporting ONT methylation files. An additional argument to `pipeline` to import modkit [output](https://github.com/nanoporetech/modkit?tab=readme-ov-file#bedmethyl-column-descriptions) would be an easier solution. Clarissa is also quite interested in...