MariaNattestad
commented
1 year ago Can you reproduce this problem with a delta file that comes from MUMmer? For example, it’s not clear if this is only happening because your script created a weird delta file that might be incorrect. And can you show the problem using any viz tools in MUMmer? Again just trying to eliminate the potential sources of the error before proceeding. Thanks!
On Thu, Nov 17, 2022 at 11:04 PM WeiWenjie @.***> wrote:
Hi Author: Assemblytics is great tool for SV calling. But I meet some problem about coordinates in negative strands: Firstly, I generated a multi-alignment-file between two genomes. And I convert maf-format to delta-format using my sript https://github.com/wjwei-handsome/scripts/blob/main/maf-convert.py.
It is noteworthy that, there is a negative-postive-strand alignment:
[image: image] https://user-images.githubusercontent.com/56633839/202638650-1a40c3ca-db2b-47cf-94ff-02fe9030af8f.png
Finally, I get the result from Assemblytics. But the insertion sequence is NOT correct according to the query_coordinates in result bed file. The actual coordinate position should be :
Coord_A = Alignment_End - (Coord_W - Alignment_Start) Coord_A == Coord_Actual; Coord_W == Coord_Wrong
Just like this: [image: C4A84F55BFFE758B8AA809C2151FAFEF] https://user-images.githubusercontent.com/56633839/202640604-a8126814-2fb0-47c9-a54e-163ae1c4f99b.jpg
PS: Sorry for my ugly simple stroke.
And I revised Assemblytics_within_alignment.py https://github.com/MariaNattestad/Assemblytics/blob/master/scripts/Assemblytics_within_alignment.py, add the judgement about strand, the result seem to be correct for me.
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Hi Maria: Assemblytics is great tool for SV calling. But I meet some problem about coordinates in negative strands: Firstly, I generated a multi-alignment-file between two genomes. And I convert maf-format to delta-format using my sript.
It is noteworthy that, there is a negative-postive-strand alignment:
Finally, I get the result from Assemblytics. But the insertion sequence is NOT correct according to the query_coordinates in result bed file. The actual coordinate position should be :
Just like this:
PS: Sorry for my ugly simple stroke.
And I revised Assemblytics_within_alignment.py, add the judgement about strand, the result seem to be correct for me.