Kris Alavattam

Results 15 comments of Kris Alavattam

Loss of *.cool 'weight' column when working with hicAdjustMatrix; possible to retain 'weight' column?

Hi, I've looked into this a bit more and it appears that, in the process of using `hicAdjustMatrix`, unbalanced counts are replaced by the balanced counts, hence the loss of...

Pearson correlation matrix

You can find the answer in this [2009 publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2858594/), among others.

conda install issues

Hi, you ought to try the installation with `mamba`, which is a reimplementation of `conda` that better handles dependency solving (among other things; [more info on `mamba`](https://github.com/mamba-org/mamba)). For example, use...

Using ComBat-Seq over RSEM estimated counts

This question is addressed here: https://www.biostars.org/p/472325/#472338

Error in setting hicPlotMatrix --vMin/--vMax

An explanation for the issue and a way to address it is described in this issue report: https://github.com/deeptools/HiCExplorer/issues/873

conda install issues

Hi, Bioconda packages are not compiled for Apple architecture, so it's necessary to instruct conda/mamba to install packages compiled for osx-64, which will then run through Rosetta. You can achieve...

hicPlotTADs error: bw file not displayed

Seems like you need to adjust the names of the chromosomes in the file. For one approach on how to do that, see [here](https://www.biostars.org/p/322341/). General Google search results for how...

isuue with mcool to hic

Some helpful workarounds described in this Biostars [forum post](https://www.biostars.org/p/360254).

Encoding problem while converting a Juicer matrix?

Any follow up on this?

Build local bias track from control with paired-end mode

Yes—see [here](https://github.com/macs3-project/MACS/issues/356#issuecomment-653692098).