4dn-dcic/docker-4dn-hic

Docker for 4DN Hi-C processing pipeline

docker-4dn-hic's Issues

How to run this pipeline in one go?

When I run docker run duplexa/4dn-hic:v43 it gives me a list of all the scripts.
How do I run the whole pipeline at once?
Do I have to run each script individually?

Empty cool and mcool files

Hi!

I am running the Hi-C Processing Pipeline on my data but I noticed some issues when generating the cool and mcool files at the matrix generation step.
While the .hic matrix looks perfectly fine by some downstream analysis, I have noticed that both .cool and .mcool files are empty. By empty, I mean that the contact matrices stored in these formats is full of zeros or NaN. However, the matrix stored in the .hic is how I would expect it. Both matrices are generated from the same pairs file.

Here I show the commands that I used to generate the .cool file:

singularity exec 4dn-hic_latest.sif cooler cload pairix -p ${THREADS} -s ${MAX_SPLIT} ${CHR_SIZE}:${BIN_SIZE} ${PAIRS} ${SAMPLE_DIR}/${SAMPLE}.cool

I think the problem occurs already when generating the .cool file in the very first step as it immediately results to be empty, I checked its emptiness by plotting the matrix as follows:

clr = cooler.Cooler('bin.cool')
mat = clr.matrix(balance=False).fetch('chr1')
plt.matshow(np.log10(mat), cmap='YlOrRd')

Also, the maximum value of the matrix is a 0.

This doesn't occur for the .hic matrix, whose plots look fine and whose matrix is not filled with 0s.

Thank you in advance for your help!

where to get /usr/local/bin/pairsqc/pairsqc.py

Hi, in the "run-pairsqc-single.sh" script, there's another py file "pairsqc.py". How should I get this one? Thanks!

isuue with mcool2hic

Hello, I could not find the code and tutorials for mcool2hic. Could you please provide some more detailed information?
Any suggestion would be greatly appreciated!