Nicolas Servant

testing cooler on capture Hi-C data

9

Hi @nvictus As quickly discussed, I tried to build a cooler object on a 3Mb Hi-C region from capture Hi-C data. I'm facing several issues according to the test I...

`cload` bug

3

Hi, I'm trying to build cool files from yeast Hi-C data, but it seems that something goes wrong with the chromosome names. Output cool file is empty because it fails...

deeptools 3.2.1 plotProfile / multiqc

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Hi, I think there is a small bug in the plotProfile output (v3.2.1) and MultiQC. ``` computeMatrix reference-point \\ --referencePoint TSS \\ -R $geneBed \\ -S ${bigwig} \\ -o ${prefix}_matrix.mat.gz...

[COOLER] new functions - balance / makebins

1

Update of the COOLER modules - New `balance` tool - New `makebins` tool - I just realized that my PR also includes an old one that I did a few...

[COOLER] run through multiple resolutions

5

Hi A small changes to allow to run the `cload` and `dump` cooler functions across multiple resolutions Thanks Nicolas

I desactivate the verbose mode in the devel_py3 branch because of a small bug in iced. The bug should be fixed soon. As soos as it is ok, go back...

Can we add the cluster option in the main config file ? Or how to deal with the cluster through the Singularity image ?

Install iced only if it is not already installed

make_viewpoint require a 4 column BED file ... Update to require only 3 columns

In some cases the --process option crashed because of a division by zero The current version fix this issue by removing the option