3DChromatin_ReplicateQC

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Hello, I am having difficulties reproducing the similarity scores reported in the paper for HiC-Spector and would be grateful for any clarification. For example, for samples G401 and A549. I...

X3N1A

ValueError when running 3DChromatin_ReplicateQC concordance

2

When running ```3DChromatin_ReplicateQC``` step by step, I came across the following problem. Both ```3DChromatin_ReplicateQC preprocess``` and ```3DChromatin_ReplicateQC qc``` generate reasonable results. But ```3DChromatin_ReplicateQC concordance``` gives ValueError: ``` Step: concordance |...

Spiridempt

The format of my input files are the same as your example files, but it can't run.

5

0 validly-mapped read pairs loaded. No valid data was loaded. Traceback (most recent call last): File "anaconda3/envs/3DC_env/bin/hifive", line 849, in main() File "anaconda3/envs/3DC_env/bin/hifive", line 93, in main run(args) File "anaconda3/envs/3DC_env/lib/python2.7/site-packages/hifive/commands/find_quasar_scores.py",...

HappyLife-together

Potential issue in wrappers/QuASAR/data_to_hifive.py

3

This may be a issue specific to me, but I had float values in my contact map which caused similar issues in [https://github.com/bxlab/hifive/issues/12](https://github.com/bxlab/hifive/issues/12) where there were no valid read data....

henrybzhang

prep function deprecated in the latest HiCRep version

2

Greetings. According to HiCRep's github (https://github.com/TaoYang-dev/hicrep/blob/master/NEWS), "prep" function is now deprecated. Is it possible to update HiCRep wrapper correspondingly? Best regards, Wenny

eternalding

Suggestions to improve the installation

2

Hi, I just installed your package. I wanted to have it installed centrally so colleagues could also use the tool. But I have encountered different issues: 1. `sklearn` & `psutil`...

cgirardot

cannot install HiCRep

1

Hi, I cannot install HiCRep using your directions (I am using R 3.6.0). My command: 3DChromatin_ReplicateQC/install_scripts/install_3DChromatin_ReplicateQC.sh --pathtopython ~/programs/anaconda2/bin/python --modules R/3.6.0 I get this error message: ========= installing HiCRep ============================================ ========================================================================...

chesi

HiC-Spector

3

And HiC-Spector doesn't work for me either with the following error: ``` Traceback (most recent call last): File "/exports/eddie3_homes_local/s1529682/3DChromatin_ReplicateQC/wrappers/HiC-Spector/run_reproducibility_v1.py", line 209, in main() File "/exports/eddie3_homes_local/s1529682/3DChromatin_ReplicateQC/wrappers/HiC-Spector/run_reproducibility_v1.py", line 202, in main get_reproducibility(M1,M2,int(sys.argv[6]))...

Phlya

Hi! Do you have any recommendation software for contact map and bins? I couldn't find any references. Thanks. Won

wyim-pgl

QuASAR-QC output folder

3

QuASAR-QC always prepends $HOME to the path of the specified folder, i.e. I ran `3DChromatin_ReplicateQC qc --running_mode sge --metadata_samples QCRep_metadata.samples --outdir ./output --methods QuASAR-QC` but it tried to save to...

Phlya