Hi Pat and co,
I have a question about Chimera.slayer and template files. We’ve been working with some pyro data that is giving us loads of chimeras when we run the dataset against the bacteria.gold.align (~59% of our sequences are eliminated after chimera checking, normally I lose about 30-45%). If I run Chimera.slayer with the template set to self, I only get 21 chimeras. Neither of these seem quite right to me… too much or too little! So here is my first question: is it inappropriate to use template=self with Chimera.slayer? After you discussed the Perseus chimera checking program in the workshop this spring, it seemed like this might be a useful way to go with Chimera.slayer too (self template) but I don’t see people discussing this anywhere on the forums or in any of the examples. Is there a reason to avoid using template=self in chimeras.slayer?
Checking the parents of the putative chimeras identified by the bacteria.gold.align template run, it appears that many of the putative chimeras are “relatives” or fabricated from relatives of organisms that are of high priority in our analyses (i.e. one common chimera parent is one of the top 3 or 4 genus we are interested in). So if these aren’t real chimeras, we definitely don’t want to exclude them from our analyses. At various points in the workshop and in the forums, people have said “one should go in and manually check chimeras after running a chimera checking program”. I have nearly 3000 chimeras to check. Thus far I’ve been opening my chimeras file in open office, sorting the sequences identified as chimeric by their parents, and then gone hunting for the most common parents. I guess I can fire them into the pintail web version and see if the sequences fall within a reasonable zone of dissimilarity against the parents. I’m daunted though, this would take me about a year to do for all my chimeras - can you offer some guidance on how to move forward on manually checking of a mammoth set of chimeras?
Best Regards,
-Joyce
PS I’m using v1.18.1