search

schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
MIT License
288 stars 28 forks source link

plot two alignments #12

Closed xbarvazx closed 2 years ago

xbarvazx commented 2 years ago

Hi,

Is it possible to plot two syri alignments together?

A vs B C vs B

How should the genome.txt file look like?

Best, Raz

mnshgl0110 commented 2 years ago

Hi Raz,

This is not supported natively, but I think it can be done.

In the genomes.txt use A, B , C, B.

For A vs B and C vs B use syri annotation. For the B vs C comparison, create a dummy annotation file which have 1bp syntenic regions between the homologous chromosomes (chromosomes having syntenic regions between the C vs B comparison would be homologous). I would assume that the 1bp syntenic region between B vs C would not be visible in the final plot given the impression that the only A vs B and C vs B are plotted.

Unfortunately, this is the best I can think of right now.

Alternatively, you may consider A vs B and B vs C comparison, which would be straightforward.

Best Manish

xbarvazx commented 2 years ago

Hi Manish,

Thanks for the answer! I will try, but now that I know I will just plan the alignments to fit the plotting, no problem.

Best, Raz