Hi, Could you please add quote=FALSE to avoid printing quotes in the segments.txt file, this is causing problems when I have "chr" in chromosome names. also would it be possible to add "#" in the header chromosome column name? so that it could be directly used in bedtools for intersect etc..
Is there a way to fix the upper limit in genome view? sometime you get a small segment maybe a telomere with very high copy gain >20 and the whole plot looks ugly, if there could be a parameter to set the upper limit to say 6, everything above 6 should be plotted at 6 and plot will look much better.
Thanks for such a good tool. Rajesh