Be sure to link to the analysis files in the readme. People should be able to click through to key files in the repo from the readme, almost like a table of contents.
The primary potential challenge I see is that low contiguity of some of these genome may thwart the ability to detect synteny. It would be good to make a histogram of scaffold lengths for each species. May suggest that some will need to be weeded out.
Hi-C - I get it!
Great start - this is a ton of work already and it is really fun to see you using all these tools together.
I suggest using GitHub markdown for knit output of rmd files, as the output is readily browsable at GitHub. More at https://rmarkdown.rstudio.com/github_document_format.html
Be sure to link to the analysis files in the readme. People should be able to click through to key files in the repo from the readme, almost like a table of contents.
The primary potential challenge I see is that low contiguity of some of these genome may thwart the ability to detect synteny. It would be good to make a histogram of scaffold lengths for each species. May suggest that some will need to be weeded out.