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Hi Aysam,
we have a strange case. We have some select params and all of them are `optional="True"`. These params are in a repeat. The first repeat element everything is fine. The second repeat we g…
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Hi,
when `transform = -log` in tracks.txt, everything's OK. Command:
`hicPlotTADs --tracks tracks.txt --region 1:20000000:22000000 --dpi 300 -out test.png`
When `transform = log`, it throws:
…
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How do you choose the best resolution? How do I know that my matrix is too sparse?
Thank you.
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I am calling this command:
`hicPlotMatrix --log1p --dpi 300 -m HepG2_150000.npz -o heatmap150000.png`
and I get
```
Traceback (most recent call last):
File "/usr/bin/hicPlotMatrix", line …
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I am facing this problem when running HiCExplorer software:
command:
hicBuildMatrix -s mapping/SRR1956527_1.bam mapping/SRR1956527_2.bam -rs dpnII_positions_GRCm38.bed -seq GATC -b hiCmatrix/SRR19…
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I am facing this problem when running HiCExplorer software:
command:
hicBuildMatrix -s mapping/SRR1956527_1.bam mapping/SRR1956527_2.bam -rs dpnII_positions_GRCm38.bed -seq GATC -b hiCmatrix/SRR19…
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The scalebar for hicPlotTADs is wrong..
```
HicExplorer Version 1.3.
MatplotLib Version 1.4.3
```
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hicPlotMatrix, without arguments, gives this help:
usage: hicPlotMatrix [-h] --matrix MATRIX [--title TITLE]
[--scoreName SCORENAME] --outFileName OUTFILENAME
…
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I have a matrix I generated in `npz`. I've realized I need to have besides of `matrix`, `chrNameList`, `startList`, `endList`, and `extraList`. What's inside them?
Thank you.
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When I'm correcting with
```
hicCorrectMatrix correct -m HepG2_150000.npz -o HepG2_150000.corrected.npz --filterThreshold -1 5 -n 10
```
I can see the following warnings. Are they normal?
`…