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Hello developers!
I notice that in your sample file (vgrna-project-paper/originals/data/transcripts/gencode29) that we download is gencode.v29.primary_assembly.annotation.gff3.gz and gencode.v29.prim…
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**1. What were you trying to do?**
I am trying to create an index for a gfa generated with PGGB.
**2. What did you want to happen?**
With the majority of the chromosomes I'm working with the …
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Hello!
I am not sure if I have missed something in the wiki or this is possible in some way I haven't quite figured out, so I am reaching out to see if you can point me in the correct direction. …
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Hello,
**What I have done**
1) Used `ppgb` to build a graph genome with the `-v` parameter to directly use `vg deconstruct` in the pipeline, to generate a .vcf file
2) Used `vcfbub` to avoid…
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Dear developers,
I wanted to try vcfbub using a pangenome of A. thaliana built using pggb.
This is the `vg deconstruct` (vg version v1.40.0 "Suardi") command stored in my `.log` file:
```
vg…
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Dear developer:
When using the module of vg autoindex, we provided the required files as required, but we still kept being reminded that we were missing the required files. May I ask how to solve thi…
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Hi Erik
I've just come across minigraph (https://github.com/lh3/minigraph) developed by the same developer of minimap2. I'm curious as to what the differences are between the graphs developed by Se…
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Hi,
When I tried to reproduce your pangenome graph, I noticed that there were several errors in vcf-merging/pangenome-graph-from-assemblies/Snakemake file, mainly about generating trio sample list …
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Hi
I've just come across a tool for enabling pangenome graph exploration using Panache, which accepts a linearised graph produced by BioGraph, given a GFA file.
https://github.com/SouthGreenPlat…
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Hi
I'm having issues getting a particular nucleotide region in my graph to be displayed using ```odgi viz```.
I set the following parameters based on the usage information:
```
odgi viz -i b…