cgirardot

hicMergeDomains bug: `list index out of range`

10

Hi me again sorry. I am again unlucky with my first try of `hicMergeDomains` (3.7.2) ``` Traceback (most recent call last): File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/bin/hicMergeDomains", line 7, in main() File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/lib/python3.8/site-packages/hicexplorer/hicMergeDomains.py", line...

hicMergeMatrixBins changes the chr size

12

I just noticed that (raw) matrices merged with `hicMergeMatrixBins` (v 3.7.2) have altered chr size. For example: The initial 1K bin matrix has: ``` hicInfo -m HiC_2-4h_R1_all-rep-merged.1Kb-bin-matrix.h5 # Matrix information...

hicAdjustMatrix ValueError: could not convert integer scalar

2

Hi, I am using the latest 3.7.2 installed via conda and I am having this error (see below) when executing `hicAdjustMatrix-3.7.2 -a keep --interIntraHandling inter -m matrix.h5 -o matrix.transRemoved.h5 --chromosomes...

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`...

Bypassing Checkout and custom read overlap : details needed

7

Dear all, I am new to this package. I have a somewhat non standard set-up with 3 fastq files : read 1, read 2 and index file. The index.fastq contains...

Extracting genomic coordinates of differential features

17

Dear chesser, I am using the code in example_analysis.ipynb to learn where the differential regions are. I am not really a python guy and would appreciate if you could help...

hints to chess extract

1

Dear, in the chess extract doc I read `we are planning to release a guide to this in the future.` Would you by any chance have a draft or few...