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Some of the steps in building syntenic blocks depend on perl codes that are difficult to install and maintain. Replace them with python equivalents.
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Hello,
Why A3A align yourself on Inter-genomic comparison synteny is 5418 gene pairs, however, A3A align another genome (V.vinifera) is 10307 gene pairs?
![1](https://user-images.githubusercontent…
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Previously, alerts were shown within each component that dynamically loaded data. There was also an alert in the main header of the page that report how many micro-synteny tracks were loaded and align…
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Despite the various benefits of computing macro-synteny blocks on-demand, pre-computed synteny blocks still have benefits of their own, such as KS values. Users should be able to choose whether to loa…
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I got the following error when running syri:
/path/syri/bin/syri -c out_m_i90_l100.coords -r ref.fa -q query.fa -k -d out_m_i90_l100.delta
any idea? thank you!
syri - WARNING - starting
multip…
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Hi,
I am using SyRI to idenitify SVs between two species (same genus, 10 Mya divergened). Here is the full command I use, but the error encounted `[W::sam_read1] Parse error at line 20
Reading BAM…
baozg updated
4 years ago
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Thanks for the great tool!
I have done some modifications to `jcvi/graphics/synteny.py` and `jcvi/graphics/glyph.py` to show `gene_legend`, add `gene names`.
However, when I use `Arrow` instead…
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Hello Haibao,
When doing self-self synteny plots, i get few gene-pairs. Is this because 1:1 hits with cscore = 1 in the plot get ignored?
Or are they just represented by the purple diagonal line…
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Hello,
when I run syri, a error masssage was reported :
syri - WARNING - starting
Reading Coords - WARNING - Chromosomes IDs do not match.
Reading Coords - WARNING - Ma…