Limitations with triple sparse format?

[Dibabbudia]

Dear Professor,
first of all thank you for the very useful tool you created. I have few questions about the triple sparse format. When I try to visualize two different matrices at the same time (not raw and iced, but different samples), I fail because I am not allowed to list more than one .bed file. So I was wondering if there is any way I could do that. And related to this, would it be possible to compare two matrices in triple sparse format that don't share the .bed file? Lastly, when I add to the command line the file with gene names (hg19.RefSeq.sorted.bed), I get in response that "Gene File (hg19.RefSeq.sorted.bed) has some missing values". Is it because there is already the matrix's .bed file? My command line looks like this:
python ~/HiCPlotter/HiCPlotter.py -f XXXXX.matrix -bed XXXXX.bed -chr 17 -n Name -o OutputFile -tri 1 -da 1 -ptr 1 -g hg19.RefSeq.sorted.bed -gl 1 -s X -e Y -r 40000
Thank you very much for any help.
Kind regards,
Davide

[akdemirlab]

Hi Davide,

Thanks for using HiCPlotter.
1- You can use multiple files sharing the same .bed file, such as below:
python ~/HiCPlotter/HiCPlotter.py -f XXXXX.matrix YYYY.matrix -bed XXXXX.bed -chr 17 -n Name1 Name2 -o OutputFile -tri 1 -da 1 -ptr 1 -g hg19.RefSeq.sorted.bed -gl 1 -s X -e Y -r 40000 -c 1
2- Currently, you cant use files with different resolutions. If you have some experience with Python coding, I can try to help you to focus which parts of the code to modify.
3- For the gene plotting, this error becomes a recurring theme so I will try to find the bug. Meanwhile, can you test your command by removing "-s X and -e Y" part to see whether you get the same error?

Best - Kadir

[Dibabbudia]

Dear Professor,
I was wondering if there is any update about the issue with the gene names file. When I add the command "-g hg19.RefSeq.sorted.bed -gl 1", I receive in response the message "Gene File (hg19.RefSeq.sorted.bed) has some missing values", even though it is structured like the one indicated in the guidelines.
Thank you very much for any feedback.
Best regards,
Davide