UPDATE: This tool now lives at GitHub
My perl script for plotting BLAST-based fragment recruitment against a reference sequence has been updated. You can now overlay up to five different queries on the same plot, allowing you to compare multiple samples to the same reference genome. I’ve also fixed a couple of bugs. Get the latest version here.
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9 Comments
First of all I want to thank you for a great script. I’m doing a metagenomics project and it will certainly come in handy for that.
There is a problem though; I can’t download the latest version of the script because the dropbox link doesn’t work. I would really appreciate it if you could fix the link so I can get it
Good job and take care!
Niklas Malmqvist
Thanks Niklas, glad to hear somebody has found it useful!
The script is now hosted at github here:
https://github.com/wilkox/blast-tools
Please don’t hesitate to let me know if you encounter any bugs or have a feature request. Just post an issue on GitHub or comment here.
Thank you, it works perfectly!
I also have a feature request:
Would it be possible to plot the identity as a scatter/dot plot instead of bars? This would help distinguish species that are related to the reference genome as they would form bands in the graph.
Once again, thank you for a great script!
I’m not totally sure what you mean by scatter plot – do you mean a synteny plot like this?
http://www.computational-genomics.net/case_studies/chlamydia_demo_03.png
Not quite, I’m thinking something like this: http://legacy.camera.calit2.net/images/help/frv/default_13.gif (that is, identity vs. genome position)
It is also very useful to be able to color the dots so that they represent fragments that correspond to a given parameter, for example “every fragment with en e-value between x and y should be green”. Is this doable as well?
Give this a try:
https://github.com/wilkox/blast-tools/tree/scatter-plot/fragment_recruitment_plotter
(note that it’s on the ‘scatter-plot’ feature branch)
Let me know if it works as expected, and I’ll add the coloured dots.
That’s exactly how I wanted it to look like, great!
Now supports custom E-value thresholds to colour the points (still on scatter-plot feature branch) – let me know how it goes.
And note that it’s been split into two scripts now – seemed to make more sense that way.