rhysf
commented
2 years ago Question1: Synima only shows synteny between pairs of genome assemblies. Therefore, if you change the order, or add different assemblies, you will plot different evidence of synteny. If you want all of the syntenic information of DAGchainer, then you could plot them all pairwise.
Question2: Synima identifies synteny based on the gene annotation that is passed to it (assuming you have used the orthology prediction pipeline included, and in the way suggested). If you are finding low levels of synteny, this may be due to poor annotation quality. You can also try running DAGchainer with reduced threshold i.e. 2 or 3 chains of orthologs.
Question3: Yes, see answer to Q1.
Question4: You can determine the order of the contigs manually from the command line or better still, the config file. You can also order the species in either way too. The genome assembly is not ordered according to length.
Synima orders the contigs by default (otherwise the plots would be a lot less clear) - and this starts from the bottom genome assembly up. However, you can control this default behavior by specifying the order of the species and the contigs - most easily done in the config file.
mudithekanayake
Hi @rhysf,
First of all, thank you very much for this awesome tool. I have some results from the Synteny output which is confusing for me. I would be grateful to you if you can answer them. I have attached 4 synteny plots. Plot 1 shows the synteny between two species (Ndig and Emu). Plot 2 shows the synteny between two different assemblies from Ndig (Flye and Nextdenovo) and Emu. In the plot 1 Ndig is Flye in the plot 2 (Plot 1 Ndig is equal to Plot 2 Flye). In the plot 3, I have changed the order of the species (Flye in the middle). Plot 4 just showing the synteny between Flye and Nextdenovo (Two genomes for the same species from two different assemblers).
Question1: Plot 1 shows the synteny between Flye (Ndig) and Emu and I am seeing lot of synteny in between (lot of lines), but when I add another Ndig genome which is Nextdenovo without changing other data, I do not see much synteny in between Flye and Emu. Number of lines are significantly different. I was wondering what is the reason for this observation?
Question2: In the plot 3 as well as in the plot 4, it is showing the synteny between the two genomes from two different assemblers for the same species. Basically they should be vary similar to each other. But, do you know why we cannot see much synteny in beween these two genomes which are supposed to be similar?
Question3: Although the plot 3 and plot 4 both show synteny between flye and nextdenovo, they seem to be different (Number of lines and the patterns of lines). Is it because there is an effect from the 3rd genome (Emu) in the 2nd plot?
Question4: In the plot 1 as well as in the plot 2, I can see the contigs in the Emu are ordered, but in all other species, the contigs are not ordered. Do you know the reason for this? Is there a way to order the other species as well? (I was wondering whether it is because the genome is ordered according to the size. But when I get my initial plot for Ndig and Emu with the default parameters the contigs were not ordered in Emu. So I think it cannot be it).
I am really sorry for asking too many questions. I am new to synteny analysis and I am still learning. So, I would be grateful to you if you can help me to solve these questions. Thank you.
config.txt1.pdf config.txt2.pdf config.txt3.pdf config.txt4.pdf