Comments (10)
@KamilSJaron got it working! Didn't have any issues running it, other than those due to my own failure to install things properly. Here are the updated plots for Species 1 for a haploid coverage of 50x and the commands I ran to get there.
FastK -v -t4 -k21 -M100 -T56 JP-Vtor-GenomeSR1_R1_001_val_1.fq.gz JP-Vtor-GenomeSR1_R2_001_val_2.fq.gz -NVtor_FastK_Table
PloidyPlot -e10 -v -T56 -oVtor_kmerpairs Vtor_FastK_Table
smudgeplot/exec/smudgeplot.py plot -n 50 -t Vtor -o Vtor_smudge2.0 Vtor_kmerpairs_text.smu
![Vtor_smudge_beta_log1 0](https://private-user-images.githubusercontent.com/111538608/264107138-6af95195-9fa3-4925-9ebf-d0ce2dadc11a.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MDQwMjY1NjYsIm5iZiI6MTcwNDAyNjI2NiwicGF0aCI6Ii8xMTE1Mzg2MDgvMjY0MTA3MTM4LTZhZjk1MTk1LTlmYTMtNDkyNS05ZWJmLWQwY2UyZGFkYzExYS5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjMxMjMxJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDIzMTIzMVQxMjM3NDZaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT03NGI4ZDIxODU4MWY1ODNhNTViOTQwZTlhZjcwZDAzNmE4NzU4NzU2NjA5Njg0MjEyZGEwNWUwMWVlNzRjOTEzJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.rGHic9XGgk6C3-XtDylXhItYm1AYyiZ1oWlsLJJZeF8)
![Vtor_smudge_beta1 0](https://private-user-images.githubusercontent.com/111538608/264107144-5f562fae-33b6-49dd-a6fe-6a7cf241abd6.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MDQwMjY1NjYsIm5iZiI6MTcwNDAyNjI2NiwicGF0aCI6Ii8xMTE1Mzg2MDgvMjY0MTA3MTQ0LTVmNTYyZmFlLTMzYjYtNDlkZC1hNmZlLTZhN2NmMjQxYWJkNi5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjMxMjMxJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDIzMTIzMVQxMjM3NDZaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT01NGExNjNmZThmZGM2YTc4M2RkNDc1ZjNkYTE1NDI1NTMzZTA4NWRjYzAwMzQxYTEwODAzZTUyYTk1ZGI3ZmU4JlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.IyFbyQfyM_ZST9K8eOopYS5lhnBRBYRE-fUjKCact2I)
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Hi,
I will give you a short answer first, and I hope I will be able to get back to you in a month or so with a lot better solution.
I think you have allotetraploid. The A <-> B divergence is already very substantial, so smudgeplot has troubles picking up the AABB signal. The thing is, Gene Myers managed to find a logical mishap we left in smudgeplot, that mishap is causing that there is a greater "drop" of the higher ploidy k-mers to the lower-ploidy brackets (namely, when there are too many overlaping variants in polyploids). Which is likely the reason, why Smudgeplot is telling you diploid. If you would like to try Genes althorithm, you can try https://github.com/thegenemyers/MERQURY.FK. But we are working on merging the two tools together, so bear with me!
Sorry for not describing it here in more detail, the explanation is very nuanced, I need to write it up properly.
But in anyway, all polyploid, and applied twice for allotetraploid, will over time go from AABB or AAAB signal, towards AB signal, as the non-recombining homoelogous genomic copies diverge. Those cases are actually the border cases we should probably call degenerated tetraploids.
I think you can quite safely use the tetraploid genomescope model, it quite nicely extimates the AABB structure.
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Thanks so much, this explanation was very helpful. I will definitely look into using Gene Myers' program and look forward to hearing more from you when you have the chance. In the meantime, I will proceed with my analysis assuming allotetraploidy.
from smudgeplot.
@weinei18 we now have a beta-version working with PloidyPlot backend and Smudgeplot front-end. If you would like to give it a try, I can send you the instructions how to get started.
from smudgeplot.
I will also close this issue for now, but do get in touch in case of anything
from smudgeplot.
@KamilSJaron Yes, I would be very interested to try the beta version!
from smudgeplot.
Excellent, presumably you already have smudgeplot, but if you don't, download the repository
git clone https://github.com/KamilSJaron/smudgeplot.git
then pull also the development branch
git pull origin sploidyplot
Now you downloaded the beta-version. There is a readme file with installation instructions and everything you need to know to run the beta-version (hopefully, it's beta after all). Let me know if it works for you.
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I reopened the issue and added it to project directory, so once you manage to get the new version plots, we can compare them here.
from smudgeplot.
Oh my gosh, thank you so much for this!!! They look amazing;
I recently found out the AB are possibly a tiny bit misplaced, I will be pushing more changes soon.
Biologically speaking, it is interesting you still have the AB smudge so strong, the smudgeplot clearly indicate a complicated genome structure; it has by far too many dups for a diploid, but too many "diploid" loci for a tetraploid, it could be as well a degenerated tetraploid or somerthing even more complex. Does look interesting! WHat's the species?
from smudgeplot.
Certainly! I will continue to check back for the new changes. I'm not able to share the species name at this time, but I can say this... Our current theory is that the ancestor of the clade was a hybrid. Old cytogenic studies and our genomescope/smudgeplot analyses show higher ploidies and weird patterns in many species within this particular genus, at least on a continental scale, and sister clades appear to be almost exclusively diploid. Divergence time is estimated to be 20-40Mya, so the degenerated tetraploid theory could fit quite nicely. Still a lot to be teased apart because there is very little information out there about them.
Thank you for your insight, it has given us a lot to consider. Very interesting indeed!
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Related Issues (20)
- Can not find R package 'smudgeplot' HOT 1
- Question about kmc parameters HOT 3
- issue about smudge_pairs HOT 3
- Smudgeplot is not suggesting an expected ploidy level HOT 2
- Salix RAD-data smudgeplots HOT 6
- estimate_1n_coverage_1d_subsets averages over two distinct high peaks
- Fix estimate_1n_coverage_highest_peak to take histogram HOT 1
- Fix plot_histograms HOT 1
- Difference between the result of smudgeplot and the real ploidy of species HOT 5
- Prepare a testing battery
- Allow other plotting styles
- FEEDBACK WANTED: Installation and running instructions for beta-version of Smudgeplot 0.3.0 Oriel HOT 6
- Issues with make exec/PloidyPlot HOT 4
- Wrong coverage estimate? HOT 4
- microsporidia smudgeplot HOT 1
- Request for feedback on smudgeplot optimization and interpretation (diploid? haploid?) HOT 6
- unclear if genome is a diploid (Smudgeplot) or pentaploid (PloidyPlot)? HOT 4
- Problems compiling (and running) smudge_pairs HOT 5
- Process was automatically killed HOT 3
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