I obtained my comparison file using blast, however when I load the comparison file on ACT it does not seem to work properly. When I select a feature (cds, inverted region) it seems to select the whole genome (everything goes yellow).. any insights?
thanks
Mathew, thank you sooo much for your replay. The thing is that I'm working with mycobacterial genomes, so the de novo assembly can create some artifacts like in the figure attached. In that case I'm assuming the assembler (Unicycler, a spades optimizer) didn't assembled this part of the genome that appears to be 'deleted' in the comparison panel, but when I analyze the bam view panel I see reads mapping in that region, so I'm calling it a 'false deletion'. Am I right in my reasoning?
My advisor suggested to try a reference guided de novo assembly, but I don know if this will work .
Again thank you!
Hi,
Yes, the top genome is the reference. This particular region codes for some matabolism related enzymes but there´s also the presence of repetitive elements like some PE/PPE proteins, and that´s the nigthmare about mycobacterial genomes and de novo assembly when using short reads. I used ACT because I needed to detect possible re-arregements like inversions and deletions. With inversions there doesn´t seem to be many artifacts related to the de novo assembly, I think the main issue is with the possible deleted areas due to missasembly. I´m thinking about following this course of action:
For detection of Inversions: de novo assembly +ACT (this way I won´t influence the orientation of my contigs by forcing a synteny with the reference)
For detection of deletions: reference guided de novo assembly +ACT (this way I can detect the fragments that are truly missing from my genome without been influenced by missasemblies).
Again, thank you for your answers!
Carolina
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