Agnieszka Golicz

VG with very large chromosomes

8

Hi, I apologize in advance for the lack of code examples but I have to estimate computational resources before starting the project and I was hoping to get some guidance....

vg rna with pggb gfa file

1

Hi, I am trying to add annotation to my graph built using pggb, but I can't seem to see the corresponding paths. I assume I must be doing something wrong....

Question about the -c fag and multi-mappers

3

Hello, I am not sure I understand the meaning of the -c flag "-c Smaller size allowed for an intron created for genes. Default: 16. We recommend to use the...

Bed file coordinate system

2

Hi, I have started using Assemblytics lately and I am trying to understand the .bed file coordinates. Are they the standard 0-based half open? Agnieszka

xTea on plant species

27

Hi, We wanted to try xTea on a plant species. Is that possible or does it require a human reference? Agnieszka

New form of variation (I think) - non-reciprocal homoeologous exchange

4

Hi Davide, This is really a feature request. We've been using VISOR and it has been great! We are working on a polyploid (allo-tetraploid) plant genome - Brassica napus. This...

Haplotype probability and read count

2

Hi, We've been trying out rpvg on a crop plant and it looks very promising! I have a question regarding inferring haplotype probability when read counts are 0. Index was...

Hi, I am trying to plot mutations from multiple individuals on the same track of circular plot. I have GRanges object that looks like this: GRanges object with 26 ranges...

AnchorWave on a very repetitive plant genome

7

Hi, I have been testing AnchorWave (v1.0.1) on a very repetitive plant genome (Faba bean, 13 Gb), but the run time has been extremely long. Alignement of a single chromosome...

Hello, Is there a preferred strategy to combine phased calls from multiple samples or genotype and phase existing SVs? All the best, Agnieszka