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I just encountered this. My GFF files only contain the feature type "gene." I wrote out the GFF files myself but they are correctly formatted according to gff3validator. I am able to run the test data…
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1. What you were trying to do
getting the graph in GFA format with vg view on the "tiny" example with simple tiny.vcf files from your test directory
2. What you wanted to happen
see above
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We need to pick a default graph serialization format for commands that write graphs. For instance, vg chunk should write another filetype by default.
I haven't looked through carefully to see all t…
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Could you provide GAF output over the nodes of the graph? Would it be possible to do? I could also submit a patch if you can describe how you'd go about setting this up.
It's defined in the minigra…
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Hello teacher, I have a question I would like to ask you, I hope you can answer it, I will be grateful! I first use HiC-Pro software and DnpII alkalase to process the HiC data, and then use EndHiC to …
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Hi !
I have followed the **Minigraph-Cactus Pangenome Pipeline** to construct a graph-based pangenome and output the index using Giraffe. Additionally, I have used Giraffe to perform read mapping f…
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I have a similar issue to the one described here: https://github.com/chhylp123/hifiasm/issues/442, but would like to understand it better. I run
`hifiasm -l 0 -o vptaxbacc_bk34-6 --seed 123 -t 48 -f…
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Hi
I'm interested in using BioGraph to linearise a GFA file produced by PGGB (https://github.com/pangenome/pggb) for visualisation in Panache (https://github.com/SouthGreenPlatform/panache). I'm cu…
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Hi Ryan,
Do you have plans to implement a graphical way to visualize e.g. a contig as a line that goes along multiple nodes? e.g. using CSV information.
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Hi folks,
I'm just trying to start my first run, so this is almost certainly user error. Can you spot my error?
config.yaml:
```cat config.yaml
#input files at top: check them!
# all input…