` hicCorrectMatrix correct` issue

[PanZiwei]

Hi, I have several questions relevant to hicCorrectMatrix correct.

1. 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?

2. 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:

hicCorrectMatrix correct \
--chromosomes chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX chrY \
--matrix hicMatrix/replicateMerged.matrix_20kb.h5 \
--filterThreshold -2 3 --perchr --outFileName hicMatrix/replicateMerged.Corrected_20kb.h5

3. 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.

When 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?

4. What is the normalisation factor generated in the log file of hicCorrectMatrix correct?

5. When I plotted the matrix at the whole genome level, the plot has only 1 column (See below). How can I fix the issue?

hicPlotMatrix \
--matrix $input_dir/WT.cool \
--log1p \
--clearMaskedBins \
--chromosomeOrder chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX chrY \
--outFileName WT.png

Thank you so much for your help!