Problems with large chromosomes

RenzoTale88 commented 4 years ago

Hello, I'm trying to run alitv using a local installation and custom json files. The files have been created and filtered through alitv.pl and alitv-filter.pl aligning 5 mammalian-size genomes chromosome by chromosome. If I try to load the smallest chromosome (<45 mb) the software works without issues. However, when I try to load larger chromosomes (50Mb and more), I get the following error:

TypeError: genome2svgScale is not a function2 AliTV.js:512:18
    getLinearKaryoCoords file:///PATH/TO/Software/AliTV/d3/js/AliTV.js:512
    drawLinear file:///PATH/TO/Software/AliTV/d3/js/AliTV.js:1000
    onload file:///PATH/TO/Software/AliTV/d3/AliTV.html:592

This regardless of adding annotations and or phylogeny tree. Is there some setting I'm missing in the alitv configuration? Like a maximum size allowed?

Thank you in advance for your help

Andrea

iimog commented 4 years ago

Hi Andrea,

thanks for reporting this issue. I've not come across this one yet. I don't see a reason for this particular error to happen dependent on the genome size. By default the sequence of large chromosomes should not be stored in the .json files. It might still be the large number of links (but you said you used alitv-filter.pl as well. How large are your .json files? Is it possible for you to share one of the json files so I can reproduce and debug the error?

Best, Markus

RenzoTale88 commented 4 years ago

Sorry, I've just realised that there was a problem in the some chromosome names in the file (for some reasons it was always naming them with the same chromosome, regardless of my script changing the instances). It's not a bug in your software. I apologise for the inconvenience, and thanks for the quick reply

Andrea

iimog commented 4 years ago

No worries, great that you were able to fix it yourself. We are happy to help when something else comes up.

Markus

AliTVTeam / AliTV

Problems with large chromosomes #155