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It may be useful to "navigate synteny" based on a gene name. For example, maybe the user story is
"I want to find BRCA1 in both human and mouse and look at the synteny"
This could involve a proc…
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Dear @tanghaibao,
I have used the following command as suggested in the wiki, and my primary objective was to identify and visualize any duplication events in the two genome. And I assumed there will…
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作者你好，我发现你在多序列微共线性模块展示了graph，peach以及cacao之间的共线性，最终绘图则是用peach和cacao都去和grape比对，那能否最终绘图能否用peach比对grape，再用grape比对cacao再用cacao比对一条其他物种的染色体这种线性的可视化方式呢，如果现在可以实现能否附一下具体步骤？万分感谢
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Hello @tanghaibao @vivekkrish @orionzhou
Recently I have read the literature (https://onlinelibrary.wiley.com/doi/10.1111/jse.12850) and conducted research on LTR- retrotransposon.
In this article,…
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Hi Yupeng,
Thanks for making MCScanX available. I'm trying to run the tool on my concatenated blast results and "gff" but I keep getting 0 matches imported and 0 discarded. Am I missing something tri…
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作者您好，我在运行 python -m jcvi.graphics.karyotype seqids layout出现了这样的报错
[10/12/24 16:34:06] DEBUG Load file `layout` …
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Greetings, I'm trying to make use of MCScanX_h, i've prepared the necessaries files following the manual yet my data neither example data is working.
My gff with 5 species gff is edited follwing t…
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Hello, got this error running de MCscan pipeline. I uploaded both .fasta and .gff3 for query and subject. (Pnotatum is the query name)
I installed with conda for Linux. Follows the traceback on stdou…
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Hi,
It is very useful tool and the graphics are amazing. However, I have some issues if you can address
1. How to add color to the synteny analysis as black and white is not appropriate
2. Is …
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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,…