Dear all, I got some confused when analyzing the Orthofinder results. I have three RNA-sequencing data for A, B,C species (A has refenrence genome and B,C haven't have a reference genome), My aim is to find the genes existed in B, C species, but absent in A species. I think Orthofinder should be work for this, after Orthofinder analysis, I got several output, one is a file called "Orthogroups.GeneCount.csv", I am not sure is this is the one that I need? The file is looks like this:
A B C Total OG0000000 28 30 13 71 OG0000001 26 31 1 58 OG0000002 6 49 0 55 OG0000003 13 40 0 53 OG0000004 18 16 18 52 OG0000005 29 19 4 52 OG0000006 18 33 0 51 OG0000007 4 46 0 50 OG0000008 28 18 4 50
I assume that OG0000002, OG0000003, OG0000006, OG0000007 is the gene that I need ?(but I am not condident if I am right or not..),
And there is another file called "Orthogroups.csv", I am confused is it tell us the correspondence for OG0000000 number and the ID in original input protein file?
Or if there is any other output file for orthofinder...(there are bunch of output files)..
Thanks in advance for your suggestions and have a great day!!