Hi all!
I need to compare aligned genomes and visualize it with dotplot. I have used Gepard and D-Genies but I don't see the possibility to add clusters IDs into the chart. Also, cause of the large alignment file it is almost impossible to add this information by myself in graphic program. I was looking for some kind of solution in R? Is there a package where I can do similar plots to those generated by Gepard?
Many thanks for any suggestions,
Best, Agata
2 answers
from the yass dna website
Well, Gepard and D-genies are doing the work but charts output are illegible. What I need is to add clusters IDs into the charts like here: https://www.researchgate.net/figure/Cluster-relationships-are-evident-in-Gepard-dotplot-alignments-using-whole-genome_fig1_239946364
I thought that it will be possible to do with those programs but I didn't find an options. Adding info in graphic program is also very hard, cause my alignment is really large. I assumed that there must be some equivalent solution in R. R can produce such a great plots with proper custom labels etc. Unfortunately it has to be dotplot. To be honest I am really stuck in here.
Log in to answer this question.
-
Plots for DNA methylation vs Gene Expression
written by sswang25 •
-
Advice on organizing large GSVA heatmap
written by Morgan S. •
-
Correlating metadata with expression based k-means cluster (in R)
written by Sebastian Hesse
-
inconsistent pan genome results with roary
written by elenaf •
-
Cluster plots from categorical clustering
written by jmah •
-
Using microarray re-annotation to combine array and Chip-Seq data
written by 2323982403 •
-
Can anyone suggest me a good pipeline to perform SNP calling on haployd organisms?
written by edoardo.piombo •
-
Bowtie2 alignment rate for 5hmC IP
written by Wet&DryImmunology
-
How can I concatenate clinical data to metagenomic results?
written by agata88
-
alpha-diversity beta-diversity rarefaction curves
written by agata88
