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gamcil / clinker

Gene cluster comparison figure generator
MIT License
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Truncating the middle of gene clusters & gene group legend #77

Open wearegroot91 opened 2 years ago

wearegroot91 commented 2 years ago
Screen Shot 2022-01-18 at 5 28 08 PM

How do I remove genes that are within the middle of the cluster? The demo.gif shows this functionality is possible but I am not sure how to actually to do within firefox.

Also, is there a way to manually add groups to the legend for genes that didn't show similarity to others?

gamcil commented 2 years ago

Hi, in the demo the gene cluster actually isn't being truncated in the middle - it consists of three different genomic loci as the cluster was found over three short genome contigs. This is done by having multiple records within a single GenBank file. To emulate that you would have to separate the A. niger region manually before feeding it into clinker.

As for the second question, you can't add groups for those genes directly through the visualisation, but you can specify groups using the -gf/--gene_functions argument. This is essentially just a two column CSV file with gene names and functions (take a look at https://github.com/gamcil/clinker/releases/tag/v0.0.23 for an example). Anything that's in that file will be added as a functional group in the plot.

neelam19051 commented 1 year ago

Hi, gamcil Sir. i want to use clinker just for few genes, is it possible to do that i mean i just wanna shows few genes which are around 30 in number in each genomes.

Thank you!