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In hicBuildMatrix is a bug concerning the computation of the cut_intervals. I have a fix for this and the test case `test_buildMatrix.test_build_matrix` is running as it should. (It is not uploaded ri…
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use case: need to estimate of fraction of reads overlapping with many regions (restriction sites)
Current solution
plotEnrichment --BED RS.bed -b Input.bam --Offset 1 --outRawCounts RS.freq -p 10
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Dear HiCExplorer,
After I build matrix with --binSize 10000 and merge with --nb 10 option which made 100000 binsize.
after that I ran hicFindTADs TAD_score with following option
hicFindTAD…
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I want to find enriched contacts between `matrix1.npz` and `matrix2.npz`. They come from different cell types. For that, I call the following command:
`hicFindEnrichedContacts --matrix matrix1.npz …
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I am interested in finding enriched contacts, for instance bins with z-scores > than 3. Specially, I want to identify enriched contacts, intra- and inter-chromosome. For this purpose, I think I should…
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The default value for the parameter `--iterNum` of the hicCorrectMatrix is set to 500. I am a little bit surprised by this high value because `Imakaev et al.` wrote in `Iterative correction of Hi-C da…
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I upgraded `HiCExplorer` version and now `hicPlotTADs` outputs (with `transform = log1p`) the following axis:
is possible in `hicPlotTADs`.
Th…
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Is it possible to get the data from `hicPlotDistVsCounts`? In a txt file, for instance.
Thanks.