Dustin Sokolowski

Gene expression and signaling role seems reversed

2

Hello! Thank you for your excellent tool. I am using CellChat to study EMT in my system and I noticed an odd discrepancy. I saw that the FN1 signalling pathway...

Clarification in input samples

3

Hello! Thank you for the exciting tool and paper. I was interested in looking into applying Bayes-Prism to a non-cancer database with a small sample size compared to TCGA. Specifically,...

Low number of collinear genes

1

Hey! Thank you for the excellent tool. I am attempting to identify syntenic blocks and tandem duplications between the mouse (mm10) and [naked mole-rat genome that I assembled ](https://rapid.ensembl.org/Heterocephalus_glaber_GCA_944319715.1/) and...

Hello and thank you for the excellent tool. I have a PB + nanopore assembly and 10X linked reads from the parents for trio binning, however I do not have...

Hey! Thank you for your great tool. I am trying to use some 10X linked reads to improve the contig assembly of a _de _novo genome completed with oxford nanopore...

Issue with SplitONT using Dorado v5 and herro V1

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Hello and thank you for the excellent tool. We have previously used verkko to generate a _de novo_ assembly using PB hifi reads, R10 ONT reads, and trios. We recently...

Script to convert gtf file to TOGA input

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Hello! Thank you for this fantastic annotation tool. I was hoping to use TOGA to annotate my rodent but using a more closely related reference species than mmus, as I...

Generating linear plots with genomealign files

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Hello! Thank you for the wonderful browser. I have three quick questions about the linear plots if you don't mind. 1) Is it possible to upload a genome align file...

Hey! I am trying to run TOGA on the SGE cluster, which relies on nextflow. My cluster has some relatively specific cluster options (see `clusterOptions`, but the amount of memory...

Using flagger for de novo primary assemblies of diploid species

5

Hello! We are working on a number of rodent assemblies from animals where we do not have trio or Hi-C-seq information. We have Hifi + (usually) ONT UL reads for...