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I freshly installed the pca branch to test out the new `hicTransform -me norm` for _Drosophila melanogaster_ genome, sadly enough, no output is created although there are no error messages, only warni…
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Hi,
I have a question regarding the mapping of genome and the chimeric reads. Kindly find time to help me.
So in the manual of Hi-C explorer, you have suggested to use BWA, I have plant genome a…
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Hi,
Do you recommend to use this [mapping pipeline](https://github.com/ArimaGenomics/mapping_pipeline/blob/master/01_mapping_arima.sh) ?
Or what is the best practice for mapping?
Thank you in a…
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Hi
I tried to use hicBuildMatrix to create of a Hi-C matrix , but something is wrong . May be I should update pysam ？Please give me some suggestions , The version I used is hicexplorer 2.2-dev .
…
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Hi All,
We (mostly @msauria) maintain another suite of 5C and HiC analysis tools implemented in Python (https://github.com/bxlab/hifive). We're interesting in exploring whether some of the novel me…
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Discovered when trying to use pyGenomeTracks:
```
Traceback (most recent call last):
File "/usr/local/bin/pyGenomeTracks", line 11, in
main(args)
File "/usr/local/lib/python3.5/dist-pack…
Phlya updated
6 years ago
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I got a mistake,when a use hicPlotMatrix to draw PCA picture,but the example show we can use it to do.
hicPlotMatrix -m ./correct_martix/correct_10kb.h5 --outFileName pca1_10k.png --perChr --pca ./h…
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In some papers, they compared the insulation score between different samples. If we can compare the separation score among different samples?
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Extending on the conversation about import/export of matrices, I think it's valid to support multiple input formats and keep only one output format. We should also deprecate liberman format support si…
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I did
```
hicConvertFormat --matrices matrix.h5 --outFileName matrix.cool --inputFormat h5 --outputFormat cool
```
It worked like a charm, but when I
```
cooler dump matrix.cool
```
…