Vivek Bhardwaj
Vivek Bhardwaj
> why do you want to hard code 10? I wanted to use the 'mapq' variable, but is not available in ChIP-seq workflow
This option will not allow users to filter for the mapq in the ChIP-seq workflow (like in DNA-mapping), only check the reads below mapq in estimatereadFiltering. So it won't be...
@LeilyR feel free to merge
Thanks a lot for the review and comments @vladsavelyev and @ewels . I understand what you say, I experienced the slow response on the output report myself when using bigger...
@vladsavelyev @ewels I've finally found time to complete the changes as requested. The multiqc module now reports sample summaries (median values), instead of per-cell summary. Also, the column headers are...
@vladsavelyev @ewels I have made all the requested changes, but the merging is still blocked with "changes requested". Please let me know if there are still unresolved issues. Thanks!
@ewels @vladsavelyev Did you find some time at the end to review the updates?
We removed HiCMarix module from hicExplorer in version 2.2 and made it a separate library. That might be the issue here. You can separately install HiCMatrix, or downgrade HiCEx version...
You can either downgrade your cooler on your main env, or create a new [conda env](https://conda.io/en/latest) with the downgraded version. ``` conda create -n hicex -c bioconda -c conda-forge hicexplorer...
yah I meant those. thanks