syntenic block membership

jtlovell / GENESPACE

Other

191 stars 27 forks source link

syntenic block membership #166

Open c-m-gibbs opened 2 months ago

c-m-gibbs commented 2 months ago

Hi there,

I have sucessfully run genespace across 4 genomes. The output in R indicated there are 694 syntenic blocks.

n regions (aggregated by 25 gene radius): 548 n blocks (collinear sets of > 5 genes): 694

I would like to learn more about the syntenic blocks - which genes are present in each block (for one of the four genomes). I am having some trouble interpretting the output files. Could someone please point me to the file/s which hold this information?

Many thanks in advance

Claire

LovellHAGSC commented 3 weeks ago

Hi Claire - I'm sorry about not getting back to you ... were you able to figure it out, or do you still have questions?

c-m-gibbs commented 3 weeks ago

Hey, no worries I never did figure it out - if you have time to point me in the right direction I would be grateful!

LovellHAGSC commented 3 weeks ago

OK ... maybe you can describe exactly what you want to get out of the data. I think the easiest thing is to read in the syntenic blast hits ... these have block ID membership. You could also explore the pangene sets, which are synteny anchored to each genome