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Hello Haibao,
A follow-up question on this. When I run
python -m jcvi.compara.synteny depth --histogram F1.F4.anchors --depthfile=F1.F4.depth
I get this
Genome F1 depths:
Depth 0: 704 of 16,…
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**Is your feature request related to a problem? Please describe.**
I've encountered a problem when using JBrowse 2's linear synteny view to observe synteny results generated by minimap2. The issue ar…
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Hi,
I was running CHROMEISTER on a plant genome against itself (~1 Gbp) where I expected to see some synteny between chromosomes, but did not see any. I then tested CHROMEISTER on a chloroplast ge…
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Sometimes hard to tell which level is which
Dotplot has a small example that says x: peach, y: grape for example, maybe be able to add something small.
Potentially could also make the two searc…
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Write a yaml validator
- Checks structure of yaml
- Checks paths lead to expected file types
- Checks gene_alignment and synteny fields can be resolved
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Hi,
I am trying to plot synteny between 5 genomes. I have calculated pairwise synteny blocks as follows:
Ref genome species 1
species 1 species 2
species 2 species 3
species 3 species 4
I …
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Thank you for developing this pipeline.
I've noticed that for my allotetraploid species, while -k 15, -k 14 works fine, once I try -k 13 or -k 12, there are a lot of broken pipeline issues. A lot …
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Is there anyway to do ks calculation for paired gene synteny in jcvi? What is the command? I saw Ks somewhere if I remember correctly but It is different to locate it?
also it there anyone to searc…
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Hi @rhysf,
First of all, thank you very much for this awesome tool. I have some results from the Synteny output which is confusing for me. I would be grateful to you if you can answer them.
I have…
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The current linear synteny code is very pairwise oriented. It needs enhancement to handle multi-way comparisons. This can be a series of pairwise comparisons (stack) but possibly over multiple windows…