agalitsyna
agalitsyna
Alternatives: - Store bam files and start from them and not fastqs? - Add parameter to start from already generated bam files? - Add auto-detection of already generated bam files...
When binning coolers, the user might provide a set of filters to include certain types of pairs into final matrices. However, for stats, there was no such option. In this...
Hi! I'm stuck with a problem that happens with my distiller-nf runs sometimes. I usually install distiller-nf from github and create conda environment from environment.yml. Then I run distiller-nf to...
If you try to create virtual 4C viewpoint in HiGlass following instructions from [docs](https://docs.higlass.io/b_viewer.html#adding-cross-sections) you get either observed over expected or inverted 4C-signal, but not proper virtual 4C. E.g. there...
With this update we: - [x] Update distiller deendencies - [x] Update Dockerfile for the most recent pairtools - [x] Introduce options for dedup Note that this code uses github...
Adding an opportunity to select the aligner out of: - minimap2 and single-end data https://github.com/open2c/distiller-nf/pull/177 - requires mapping with parse2 instead of parse - bwa mem2 which is a fast...
I included here only the issues that are either easy small fixes or structural changes that are important and also easy to introduce. - [ ] Support minimap2, bwa aln,...
Problem: we want to calculate scalings, compartment score, and insulation o the maps generated from simulations. Should we include these functions into polychrom, or rely on and support them in...
build `stats` CLI that will report [pairtools-like stats](https://github.com/open2c/pairtools/blob/master/pairtools/cli/stats.py): - nnz per region (cis); per pair of regions ("trans"); in total - fraction of contacts per region; per pair of regions...