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jasminezhoulab / TopDom

TopDom is a software tool to ideintify Topological Domains, which are basic builiding blocks of genome structrue. TopDom is computationally very efficient. Using detecting optimal polygon algorithm, TopDom detect topological domains in a linear time. As well as, this tool requires only a single parameter, which enable user to use easily.
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Input File Format Issue #2

Open anupambh opened 4 years ago

anupambh commented 4 years ago

Hi, I am highly interested to run TopDom for identifying TAD in Hi-C data. I am using HiC Explorer to generate matrix file in h5 format.

I am also attaching the HiCexplorer command for your information: The command to build HiC matrix:

/opt/miniconda2/bin/hicBuildMatrix --samFiles SRR400251_1.bam SRR400251_2.bam --binSize 10000 --restrictionSequence GATC --outBam SRR400251_chr10.bam --outFileName SRR400251_chr10 --threads 40 --inputBufferSize 400000 --region chr10

As per the manual of TopDom, The input matrix should be like :

CHR from.Coordinates to.coordinates Values Values...

The TopDom program is running successfully in the demo dataset included in your program.

How Would I convert the corrected matrix.h5 to TopDom specified format?

Please suggest to me how to make the file format for the TopDom program.

Thanks in advance. Regards; Anupam Research Scholar Bioinformatics Department IASST, India

TheCatalyticMicroChip commented 3 years ago

Hi Anupam,

Did you manage to figure this out? I am struggling to convert the sparse matrix to N × (N + 3) matrix.

Mzwanele

anupambh commented 3 years ago

Hi Mzwanele, I didn't figure out how to resolve that issue. I was not using TopDom anymore, as there is not much support from the developer.

TheCatalyticMicroChip commented 3 years ago

That's too bad. It's such a good package. Thanks