Sizes between inversions do not correspond across the genome

[JAEYOONSUNG]

Hello! I obtained figures comparing three genomes using minimap2, SyRI, and plotsr. However, there seem to be issues where the sizes between inversions do not correspond and the representation of synteny is not detailed enough and appears too clustered. Is there a specific part of the command that I should modify to address these problems?

[mnshgl0110]

You can use --invgaplen option of syri to adjust inversion selection.

I do not understand what do you mean by less details for syntenic regions. Could you please describe it?

[StanaW]

Hello! I came across the same problem with the sizes between inversions not corresponding. I was trying to search through the tool on the usage of --invgaplen, but I cannot find it. What do you specify as an argument? And how can I filter out inversions with very different sizes? Thank you for your help!

[mnshgl0110]

I was trying to search through the tool on the usage of --invgaplen, but I cannot find it. What do you specify as an argument?

--invgaplen is a parameter for syri. So you would need to rerun syri with this parameter if you do not want inversions with large indels.

And how can I filter out inversions with very different sizes?

Rerun syri with the --invgaplen parameter. Or you can filter the input files for plotsr (for example: syri.out file) to remove such inversions with awk.

[StanaW]

Thank you so much for your response! Yes, I wanted to rerun syri. But my question is what do you specify as the argument for the parameter "--invgaplen"? Is it the size you do not want the inversions to exceed?

[mnshgl0110]

Output from syri -h:

 --invgaplen INVGL     Maximum allowed gap-length between two alignments of a multi-alignment inversion. It affects the selection
                        of large inversions that can have different length in the reference and query genomes. (default:
                        1000000000)

So you have to specify a number.

[StanaW]

Thank you so much! I am sorry, I have not noticed it there.