Entering edit mode
2.7 years ago
alslonik
▴
310
Hi all
I am trying to construct ancestral chromosomes using ANGeS for 8 plant genomes, and having problems with the input marker file. I have Orthofinder output as well as MCscan and trying to combine the outputs to get the Marker file as shown in the examples of the software. The problem is the the collinearity blocks (from MCscan) are for pairs of genomes and not for all the 8 genomes, and preparing the blocks based on orthologs (from Orthofinder output) makes the blocks too short for ANGeS. I use R and command line to change the formats usually. Has anybody here had the same experience and could show me the way?
Many thanks
Did you figure out how to answer your question? I am just curious because we are teaching ourselves how to perform such an analysis. But we are little stuck at the MC-SCAN-X step because we are not sure what "epoch" means for the various flavors of MC-SCAN packages. Could you briefly explain or provide any link(s) / example(s) about this epoch concept? Thanks!
Hi, not really, no. Still unanswered. What do you mean by "epoch"? I have run MCscan X several times and do not think that I had anything called "epoch" in the process.
Have you identified a way?