Only few genes are being linked

[githubgig]

Hello,

I am trying to use NGenomeSyn to get the gene synteny map of the two scaffolds. Scaffolds A.fasta with 11 genes and B.fasta with 32 genes. All 11 genes in scaffold A are also present in scaffold B, but when i run GetTwoGenomeSyn.pl, only three genes are being linked. Please see attached image. The command I am using is below:

GetTwoGenomeSyn.pl -InGenomeA A.fasta -InGenomeB B.fasta -OutPrefix Out -MappingBin minimap2 -MinLenA 5000 -MinLenB 5000

I also tried with minlen 1000, but the results are the same.

I dont get any errors on screen. How can i rectify this?

Thanks.

[hewm2008]

【A: For distantly related species, gene and protein alignment are generally used (blastp, diamondg, and then mcscan is used to find collinear blocks).
B: For closely related species, direct genome data analysis is used. (Generally, for genomes of different varieties within the same species, minimap2 and mummer are used to find collinear regions.)
If the two species are too distantly related and no collinear blocks are found from DNA using this program, it is recommended to first find collinear blocks using proteins.

you can run the mcscanX firsrt