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Hi,
I have aligned my reads using bwa and have reordered them as well using picard tools.
Also, I have removed PCR duplicates and reads with MAPQ
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pyBigWig lists as dependency numpy version 1.12, however, numpy version 1.15 is the newest one and 1.14 is missing too.
Furthermore, a version for Python 3.7 is missing. Is there any way to enforce …
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Hi
I want to plot enriched contacts (or loops) in hicexplorer , just like **Aggregate Peak Analysis** in [juicer](https://github.com/aidenlab/juicer/wiki/APA) . I think the function **hicAggregateC…
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when I used hicFindTADs to detecte TADs，The following parameters that I couldn't understand . minDepth and maxDepth, The software's suggestion just a range.so when I try different parameters, the resu…
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Hello,
I am getting a unicode error similar to the one that appears in issue #174 when trying to run hicBuildMatrix. None of my file names have non-ASCII/non-standard characters as far as I am aware,…
hwick updated
5 years ago
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I "pip3 install mikado" installed the mikado on our hpc cluster and used the "sample_data" to test it from command line. I got same error as "https://github.com/EI-CoreBioinformatics/mikado/issues/164…
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Hi,
I have used following command to generate Hi-C matrix but it fails to give a matrix. However, the bam file is generated.
qig hicBuildMatrix --samFiles file7.bam file8.bam --QCfolder hicU1 -…
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Hi,
I have installed hicexplorer using conda. The version that is installed is hicexplorer 2.2.1
However, when I look into the functionality of hicBuildmatrix using help I see following options
…
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I want to plot one loop which were called by Juicer using `hicAggregateContacts` . But when I run
> hicAggregateContacts --matrix ../data/WSKAT7_10000_norm.h5 --BED ./loop_test.bed \
--outFileName…
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Hello,
Thanks for HiCExplorer!
I'd like to report one problem I had when trying to convert from hic or cool format to hdf5. Here is what I did:
1. I have hic files that I'd like to convert to…