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estebanpw / chromeister

A dotplot generator for large chromosomes
GNU General Public License v3.0
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Breakpoint about inversion #26

Closed Chenglin20170390 closed 2 years ago

Chenglin20170390 commented 2 years ago

Hello Esteban,

Many thanks for developing such useful tools.

1). I would like to use  chromeister to check inversion and their breakpoint (first figure).  Does chromeister can highlight or report the breakpoint of inversion in the png? 
2). When I use chromeister to check the small inversion event, I find the figure not like dotpoint(second figure), but dotline. it's because of  k-mer size?  

 Thanks.
inv breakpoint image

best, Lin

estebanpw commented 2 years ago

Hello Lin! thanks for your feedback :)

Regarding 1) if I understand correctly you want to have the coordinates of the inversions? There is approximate support for that (see here and also more details and a tutorial here. Note that by approximate I mean that CHROMEISTER loses a lot of precision while scaling down the comparison, so the breakpoint's coordinates will be approximate in plus/minus several thousand base pairs. If this is not good enough, I suggest you use GECKO for the particular region.

Regarding 2) I think this is a problem related to the visualization given the size of the sequences. CHROMEISTER is aimed at comparing chromosomes (although it also works for small ~1MB sequences). According to the coordinates in the plot, the sequences appear to be around 3,000 base pairs. In that case I recommend to run GECKO or BLAST. In fact, you can find information on how to do this on the Galaxy workflow manager here for free and without requiring command line.

Also, please note that at the moment I am unable to dedicate much time to this repo but if needed I will take a closer look during the weekend. Let me know if this helps!

Bests, Esteban

Chenglin20170390 commented 2 years ago

Thanks, I will try it.