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slt666666 / gene-cluster-matrix

Visualize gene clusters & its phylogenetic relationships by interactive matrix figure.
MIT License
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Application question? #1

Open cahuparo opened 1 year ago

cahuparo commented 1 year ago

Hi Toshiyuki,

Congrats on developing this tool! I have a question on potential application of this gene cluster analysis:

I have RenSeq contigs and gene models. I would like to map them to a reference genome and generate this type of matrix or learn about their location in the genome overall.

a) Should I map the renseq transcript models to the genome assembly using something like exonerate?

b)What tool do you suggest to use for mapping and generating the gff3 file required here?

c) Would it be possible to scale up to more than one chromosome?

Thanks!

Camilo

slt666666 commented 1 year ago

Hi Camilo,

Thank you for your comments. a), b) Yes, this gene cluster analysis calculates the genetic distance between genes(or mRNA...etc). So, we should provide information about the position of genes of interest as gff3 format or csv format. If tools generate gff3 file with Name tag in attributes field, it's perfect for my analysis. (I don't know what tool is the best, I'll survey it...!)

c) Yes, this analysis applied to all chromosomes.

Best, Toshi