Nothing in the output figure

marbl / ModDotPlot

MIT License

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Nothing in the output figure #32

Closed jiadong324 closed 1 month ago

jiadong324 commented 3 months ago

Dear author,

Thanks for developing this nice visualization tool!

I am trying to make a plot between two sequences. The dotplot below is obtained with simple k-mer matches.

But when I use moddotplot for these two sequences, I got the figure below. This is my command moddotplot static -f NA12877_pat-0000377_chr22.fa --no-hist --no-bed -o dotplot --compare

NA12877_pat-0000377_CHM13-chr22_distal

Is this the parameter issues or something else?

alexsweeten commented 2 months ago

Hi @jiadong324,

Sorry for the late response! While I don't have your sequences in front of me, my best guess is that this is likely a result of one fasta being upper case, and the other being lower case. I've since patched this #33

Please update to v0.8.5 and try again. If it's still outputting a blank plot, please let me know!

Alex

jiadong324 commented 1 month ago

@alexsweeten Thanks, it works now with the latest version.

I also tried --grid with --compare-only, it generates all pairwise comparison as individual figures. If I understand correctly, this option should generate a grid like figure including all the sequence comparisons.