Comments (6)
I don't have any ideas of mc changes that would affect Panacus. Here's two yeast graphs made with Cactus v2.6.4 (which was used for the v1.1 HPRC graphs) and Cactus v2.7.0 (which is the current release).
If there's a regression, I would think it would show up between these two graphs.
http://public.gi.ucsc.edu/~hickey/debug/panacus/
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Thanks for reporting! Can you provide a graph where I can debug the issue?
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Thanks @glennhickey!
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Panacus runs smoothly on these graphs (see attached files). @Xuelei-Dai could you describe the specific issue in more detail and provide a graph that does not work with the current release of panacus?
yeast-v2.6.4.histgrowth.all.html.gz
yeast-v2.6.4.histgrowth.all.html.log.gz
yeast-v2.6.4.histgrowth.all.pdf
yeast-v2.6.4.histgrowth.all.tsv.gz
yeast-v2.6.4.histgrowth.all.tsv.log.gz
yeast-v2.7.0.histgrowth.all.html.gz
yeast-v2.7.0.histgrowth.all.html.log.gz
yeast-v2.7.0.histgrowth.all.pdf
yeast-v2.7.0.histgrowth.all.tsv.gz
yeast-v2.7.0.histgrowth.all.tsv.log.gz
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Thanks @danydoerr and @glennhickey!
In the current version of Mingraph-Cactus (MC), the gfa file does not have P
line, and the new W
line was changed. Since I referred to the Pangenome Coverage and Growth Statistics
pipeline (convert the 1.1 version of gfa
to 1.0 (vg convert -gfW
)), recently I directly used the 1.1 version of the gfa
file as the input of panacus
, it's okay. So I suggest that you can add some instructions to your pipeline, for example, how should the gfa
1.1 version be run?
Best,
Xuelei
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That's a good point, @Xuelei-Dai, the current README does not contain an example for the MC graph. I have now added an example for the MC graph.
To be perfectly clear, panacus
has always supported GFA 1.1 and therefore also the latest MC graphs. Neither any update is required, nor any bug to be fixed. The example in the README suggests to visualize pangenome growth only for a subset of samples (those corresponding to haplotypes). This preprocessing is not part of panacus
and remains the responsibility of the users.
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Related Issues (20)
- Option to output plots in separate PNG files HOT 11
- Could you please make an new release? HOT 3
- command is not supported for more than 65534 HOT 6
- How to Visualize the results of the minigraph-cactus? HOT 21
- Feature request: Alternative plot with #nodes/#edges vs AC
- A problem while running panacus-visualize HOT 1
- Update Readme to reflect installation of python dependencies in the installation section. HOT 1
- compiler error in rustc-serialize HOT 3
- Haplotype labels in TSV, visualisations ? HOT 8
- panacus-visualize.py is overwhelmed by 1000 haplotypes HOT 10
- how is panacus treating Ns HOT 4
- Discrepancy between graph length, reference length, and novel base pairs HOT 3
- macOS binary missing HOT 1
- What does the output content represent HOT 7
- could you give us an example of cactus? HOT 7
- Installation instructions HOT 2
- Merge different chroms stats into one graph HOT 3
- path coordinates HOT 8
- After `panacus hist` and `panacus growth`, the final visualization will show `#nodes` instead of `bps`. I use `-c bp` for hist HOT 1
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