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jtlovell / GENESPACE

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non-syntenic chromosomes in the plot #43

Closed aberaslop closed 2 years ago

aberaslop commented 2 years ago

Hi! A pleasure to use GENESPACE, as always. I was wondering if there is any way to have non-syntenic chromosomes still depicted on the plot. I have a set of 6 genomes with different numbers of chromosomes, and when making the plot, those not sharing genes, are not shown. Thanks!! L.

jtlovell commented 2 years ago

I'n not sure I'm following ... are you missing the segments of those chromosomes in your riparian plot? Maybe post an image of the issue?

aberaslop commented 2 years ago

Hi John,

Sorry, I was not very clear. I realized that some contigs (not all of my fragments are full chromosomes) in some genomes were missing from the plot. Further inspection revealed that those missing fragments were always short-ish (shorter than 200,000bp), and had few genes (as reported in the gff). Looking up information about another issue, I found part of the solution here #24. Decreasing minGenes2plot makes some of those fragments appear in the plot. I consider this to be the answer, so I think we can close the issue. Thank you!