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Hi, while exporting .h5 matrix to .cool matrix from fly genome noticed that .cool format has difficulty accepting chromosome names since they are combination of numbers and letters and the word 'chr' …
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I am really fond of pyGenomeTracks and hicPlotTADs to view Hi-C data, but when exploring multiple matrices at long ranges to find loops, I think HiGlass is very handy!
I saw that `hicConvertFormat`…
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[S1_ILLUMINA.merge.dedup.realign.recal.snpeff.stats.summary.txt](https://github.com/ewels/MultiQC/files/293944/S1_ILLUMINA.merge.dedup.realign.recal.snpeff.stats.summary.txt)
Hello Phil,
I am trying t…
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Dear HiCExplorer team,
I'm using version 2.1.3 (Python 3.6 environment).
Can you help me to interpret 'WARNING:hicexplorer.HiCMatrix:Bin size is not homogeneous' printed to stderr from running…
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Hi, any reason pysam dependency is set strictly to `pysam==0.11.*`? This is incompatible with pyGenomeTracks, which requires `pysam>=0.14`.
Phlya updated
6 years ago
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I want to save the pixels and the bins and I get the following error. I do not want to extend anything, I want to create a new cooler file with `cooler.io.create`. I do not really understand the error…
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Below are open issues for our hackathon. Please feel encouraged to add to them:
## Major
- [x] Conda directive in rules
- [x] DNA: Vivek
- [x] ChIP-seq: Devon
- [x] ATAC-seq: Devon
- […
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Hi,
I am analyzing capture Hi-C data, so I wanted to build a matrix only for the region that's enriched in the experiment. In principle, `hicBuildMatrix` offers this option with the parameter `--re…
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Subject: Red the docs fails to build
### Problem
- I wanted to build the read the docs files, but it is crashing with the error message below. I asked already the sphinx project, they recommended …
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Hi
To compute the A / B compartments ,I used hicPCA and get pca1.bedgraph , pca2.bedgraph. I'm very confused about the two bedgraph files .
For example , In one bedgraph there is chr1 520000 5…