Closed Wenwen012345 closed 1 year ago
I'm pleased you have time to test the collinearity detection from WGDI. My approach was to first extract all synteny blocks that appear collinear in the homologous dotplot generated with the '-d' parameter. Then I aimed to filter out unwanted synteny blocks by running WGDI again with the '-c' parameter. The two scenarios you mentioned arise from tandem that occur within the same genomes. These situations would not emerge in interspecific comparisons across different genomes. The '-c' parameter in WGDI can be used with 'tandem = false' to remove these synteny blocks caused by tandem. The '-bk' parameter allows you to inspect the filtered blocks that remain afterward.
OK. I will consider! Thanks!
Dear @SunPengChuan
Recently I've been using WGDI software. But something is confusing me, mainly about the colinearity (-icl).
The number of colinearity blocks found by the MCscanX I'm using is 583, and the number of colinearity blocks found by using WGDI is 1642 (parameters below). This makes me puzzled. Then I checked the colinearity block file generated by WGDI. Then I found some possible problems and would like you to comment on them?
For example, some of the colinearity blocks seem to be false positives. Some of the colinearity blocks are simply genes in the opposite order and written there;
Then there are colinearity that seem to simply "slide" a gene, as follows.
But these problems do not seem to exist in the MCscanX results. These may be the reason why there are more blocks in the "WGDI -icl" results than MCscanX results.
Best Regards! Sincerely, Wen
Attached: Rb.collinearity.txt MCscanX reresults Rb.wgdi.collinearity.txt Rb2.conf.txt