scoutzxb
commented
6 years ago Hi Ilya,
Thanks very much for your suggestions. I'm currently working on the next version of CscoreTool, and I'll consider adding these features in it.
Best,
Xiaobin
On Thu, Jan 18, 2018 at 9:22 AM, Ilya Flyamer notifications@github.com wrote:
Hello, thank a lot for this tool! I have started trying it and the results look very promising!
However, I have a couple of suggestions which would make using this tool much simpler. I would be happy if you could have a look at them and consider implementing these features. Unfortunately, I don't know C/C++, so can't help with this...
1.
More options for input. For example, a cooler file ( https://github.com/mirnylab/cooler https://github.com/mirnylab/cooler) should have all the information this programme needs: binned data with weights already usually calculated, since it has its own balancing method. Also, even with the current input format, it would be great to allow getting the data from stdin instead of a file on the disk (this way slightly different formats, e.g. with different column order, can be re-formatted in a stream without saving to disk). 2.
Seems like C-score is oriented randomly for each chromosome, same as eigenvectors. However an easy method to fix this is to have a separate track associated with activity (for example, GC-content), to flip the values to have a positive correlation with that track for each chromosome. It would be very convenient if this was implemented directly in CscoreTool without any need of post-processing.
Thank again for creating this tool!
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liufuyan2016
Phlya
Hello, thank a lot for this tool! I have started trying it and the results look very promising!
However, I have a couple of suggestions which would make using this tool much simpler. I would be happy if you could have a look at them and consider implementing these features. Unfortunately, I don't know C/C++, so can't help with this...
More options for input. For example, a cooler file (https://github.com/mirnylab/cooler) should have all the information this programme needs: binned data with weights already usually calculated, since it has its own balancing method. Also, even with the current input format, it would be great to allow getting the data from stdin instead of a file on the disk (this way slightly different formats, e.g. with different column order, can be re-formatted in a stream without saving to disk).
Seems like C-score is oriented randomly for each chromosome, same as eigenvectors. However an easy method to fix this is to have a separate track associated with activity (for example, GC-content), to flip the values to have a positive correlation with that track for each chromosome. It would be very convenient if this was implemented directly in CscoreTool without any need of post-processing.
Thank again for creating this tool!