Breakpoint about inversion

[estebanpw]

Breakpoint about inversion

[estebanpw]

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]

Thanks, I will try it.