Hi,
I have several questions relevant to hicCorrectMatrix correct.
The coverage histogram of my data showed that the count bins are not well distributed and didn't strictly follow the Gaussian bell. How can I decide the best threshold? Can I still use the vertical line -3.2 as the lower cutoff?
I run the correction with hicCorrectMatrix correct --filterThreshold -3.4 5.0 --perchr, but I encountered the error below
ERROR: iterative correction:*Error* matrix correction produced extremely large values.
This is often caused by bins of low counts. Use a more stringent filtering of bins.
Hi, I have several questions relevant to
hicCorrectMatrix correct
.The coverage histogram of my data showed that the count bins are not well distributed and didn't strictly follow the Gaussian bell. How can I decide the best threshold? Can I still use the vertical line -3.2 as the lower cutoff?![image](https://user-images.githubusercontent.com/44417006/188532828-f588f0ff-4e90-44db-ab8d-d66f250e92e6.png)
What's the difference with or without
--perchr
?In https://hicexplorer.readthedocs.io/en/latest/content/example_usage.html#correction-of-hi-c-matrix:
hicCorrectMatrix correct -m hic_matrix.h5 --filterThreshold -1.5 5 -o hic_corrected.h5
But in example usage:I run the correction with
hicCorrectMatrix correct --filterThreshold -3.4 5.0 --perchr
, but I encountered the error belowWhen I checked your suggestion https://github.com/deeptools/HiCExplorer/issues/117#issuecomment-324861282, I found I had a similar case that my "chromosome Y is having more or less 0 counts in its bins" as you described in example case. How can I solve the error?
What is the normalisation factor generated in the log file of
hicCorrectMatrix correct
?When I plotted the matrix at the whole genome level, the plot has only 1 column (See below). How can I fix the issue?
Thank you so much for your help!