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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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hicMergeTADbins is missing #363

Closed QianzhaoJ closed 5 years ago

QianzhaoJ commented 5 years ago

Hi : I installed HiCExplorer using conda and the version is 2.2 . I want to use the function hicMergeTADbins ,But I found the command is missing . When I typed hicexplorer -h , I looked

The following is the list of tools: findRestSites Identifies the genomic locations of restriction sites hicBuildMatrix Creates a Hi-C matrix using the aligned BAM files of the Hi-C sequencing reads hicQC Plots QC measures from the output of hicBuildMatrix hicCorrectMatrix Uses iterative correction to remove biases from a Hi-C matrix hicFindEnrichedContacts Identifies enriched Hi-C contacts hicCorrelate Computes and visualizes the correlation of Hi-C matrices hicFindTADs Identifies Topologically Associating Domains (TADs) hicMergeMatrixBins Merges consecutive bins on a Hi-C matrix to reduce resolution hicPCA Computes the principal components (eigenvectors) for A/B compartment analysis hicTransform Computes obs_exp (like Lieberman-Aiden), pearson and covariance matrix for A/B compartment analysis hicPlotDistVsCounts Plot the decay in interaction frequency with distance hicPlotMatrix Plots a Hi-C matrix as a heatmap and can add a pca track to it hicPlotTADs Plots TADs as a track that can be combined with other tracks (genes, signal, interactions) hicPlotViewpoint Plots the number of interactions around a reference point hicSumMatrices Adds Hi-C matrices of the same size hicPlotDistVsCounts Plots distance vs. Hi-C counts of corrected data hicInfo Shows information about a Hi-C matrix (no. of bins, bin length, sum, max, min, etc) hicCompareMatrices Computes difference or ratio between two matrices hicAdjustMatrix Remove, keep or mask specific regions in a matrix hicAverageRegions Sum up defined reference points and a range up/downstream of it. Useful for TAD analysis hicPlotAverageRegions Plot tool for hicAverageRegions hicNormalize Normalizes matrices to 0 1 range or to lowest read coverage hicConvertFormat Converter for different interaction matrix file formats.

hicMergeTADbins doesn't exist . It is so confusing because I find hicMergeTADbins in github , may be I should install it from github ? Many thanks !

joachimwolff commented 5 years ago

Hi,

this script is from the previous main developers of HiCExplorer, it was created back in November 16 but was never added to 'setup.py' and is therefore missing. There are no test cases for this tool too, which means I cannot tell you if this is some working script and it was simply not added to setup.py or it was accidentally merged to master. Could be there are some issues with Python 3 too.

I think it is the best to use it from github and test it on your own if it works, any feedback is welcome.

Best,

Joachim