Comments (8)
panacus
does not make use of node annotations, if that is what you mean. It uses the sequence underlying the nodes as reference for the coordinates. In other words, path coordinates should work in pggb
as well as Minigraph-Cactus
, and I have tested it on both. Does it not work for you?
from panacus.
No. It did work with my pggb graph. Here is the command I use:
panacus hist -c bp -e Col-0.CEN.bed -H -t 12 ../At_Chr1_p90_s10000/panCEN.Chr1.fa.gz.f6e6337.f85392c.20baff7.smooth.final.gfa > Chr1.hist
And here is the bed info
Col-0#Chr1 14842915 17129565
Col-0#Chr2 5281568 5281745
Col-0#Chr3 13596521 15747999
Col-0#Chr4 5256168 5256346
Col-0#Chr5 12395998 14812445
from panacus.
Can you send me the graph, too?
from panacus.
The graph is quite large, could I send you a link by email?
from panacus.
Yes--Just sent you an email, so you have mine.
from panacus.
Thanks! Sent it. By the way, what's the exact meaning of quorum?
from panacus.
Quorum sets the number of paths/groups that must share the counted graph feature when going from n to n+1. The simplest way to understand quorum when it is set to 100%, i.e, -q 1
. In that case, panacus
would count only those graph features that are shared by all paths/groups. This is commonly known as core
pangenome. Setting -q 0.5
is also known as shell pangenome and -q 0.1
cloud pangenome. Here are some more explanations: https://hackmd.io/asojhSf-T8GOJOr9HQj_IA#Panacus
from panacus.
Actually, panacus
run successfully with BED. The error is because I use whole genome bed for chr1 graph.
from panacus.
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
- Request software updates HOT 6
- 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
- AttributeError: 'DataFrame' object has no attribute 'cumulative' HOT 13
- 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
- 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
- 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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from panacus.