Closed salmanento closed 8 months ago
There seems to be a problem when handling gff files, specifically regarding the alignment between the initial two columns in the blast file and the second column within the gff file.
Thank you, resolved. Dotplot created, Please check it is Ok? Can you please help me how to interpret the dotplot results?
Your results show no significant collinearity between the two species. Could their divergence be too great? Consider using closer species to check if it’s a data processing issue.
What about these results now?
The reason why the second figure doesn’t have clear synteny blocks is leading to incorrect results in your subsequent analysis.
Now, I have used two closely related species, belonging from same genus. Look into the results please.
I am trying to create dotplot using two genomes for whole genome duplication detection. I am facing issue (ValueError: cannot reindex on an axis with duplicate labels) screenshot of error attached. I have also attached the Screenshot of GFF1, GFF2, Lens1 & Lens2 & Blast files used. Please look into it and guide about the issue and make me able to proceed with the analysis.
Below is the total.conf script [dotplot] blast = /home/lilin/wgd-exp/dotplot/updated/blastp_output.blast gff1 =/home/lilin/wgd-exp/dotplot/updated/X.ripnewide_gene.gff gff2 = /home/lilin/wgd-exp/dotplot/updated/S. gregaria_updatedgene.gff lens1 = /home/lilin/wgd-exp/dotplot/updated/lens1_X.riparia.lens lens2 =/home/lilin/wgd-exp/dotplot/updated/lens2_S.gregaria.lens genome1_name = Xya_riparia genome2_name = Schistocerca_gregaria multiple = 1 score = 100 evalue = 1e-5 repeat_number = 10 position = order blast_reverse = false ancestor_left = none ancestor_top = none markersize = 0.5 figsize = 10,10 savefig = /home/lilin/wgd-exp/dotplot/updated/dotplot.png
Attachments
![BlAST](https://github.com/SunPengChuan/wgdi/assets/147240366/4a1866de-7a48-4ecb-a911-65ac18c14425)