No Syntenic Depth for Orthogroups

[manoharbisht1998]

Hi,
I have used the following command to generate a syntenic depth plot across intra- and interspecific comparisons in my species. I got all the outputs except the syntenic depth plot.
wgd syn wgd_ortho/Orthogroups.sp.tsv -ks wgd_ortho_ks/Orthogroups.sp.tsv.ks.tsv Aquilegia_coerulea.gff3 --additionalgffinfo 'mRNA;Name' Protea_cynaroides.gff3 --additionalgffinfo 'mRNA;ID' Acorus_americanus.gff3 --additionalgffinfo 'mRNA;Name' Vitis_vinifera.gff3 --additionalgffinfo 'mRNA;Name' -o wgd_ortho_syn
Also, is there any way to reduce the noise in the overall species dot plot?

Thanks

[heche-psb]

Hi, could you please share the full log of your run? That will help me pinpoint issues. One solution to reduce noise is that you can use a more stringent e-value to filter out low-similarity homologous pairs.