TADbit
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3DGenomes
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like ma...
Hi again, David: This might (probably) be related to this previous issue https://github.com/3DGenomes/TADbit/issues/377#issue-1294458520 When I get raw matrices for a same chromosome using the TADbit Python API and using TADbit...
Hello, I am currently trying to install TADbit by building from the Dockerfile within the _containers_ folder. To do so, I cloned the repo locally and created an empty folder,...
Hi, I am trying to test modelling with following command: tadbit model --workdir model_Ctrl_test --input_matrix test_Ctrl_matrix.f.bed --noX --optimize --beg 0 --end 20000000 --reso 50000 --maxdist 2000:4000:100 --nmodels 20 --nkeep 20...
Hello, I get the following error while running oneD normalization: Error in formula.character(object, env = baseenv()) : invalid formula "\"tot ~ s(map) + s(cg) + s(res)\"": not a call Calls:...
Hello, After generating interaction matrices I have saved them through hic_map function in .mat format. I would like to use the matrices for the downstream analysis, in Python, however I...
Hi, What if I already have bowtie2 aligned .bam file or filtered pairs file, wanna using tadbit to call tad? How to make tadbit required bam format file from normal...
Hello, I try to export files using tadbit export and I am getting the follwoing error: tadbit: error: invalid choice: 'export' (choose from 'map', 'parse', 'filter', 'describe', 'clean', 'normalize', 'bin',...
In the tutorial (http://3dgenomes.github.io/TADbit/tutorial/tutorial_1-Retrieve_published_HiC_datasets.html), is the command ` fastq-dump -A SRR5344921 -DQ '+' --defline-seq '@$ac.$si' -X 100000000 --split-files --outdir FASTQs/` But the `-DQ` option doesn't seem to be in `fastq-dump`...
Hello, After I installed the TADdyn, I wanna try the test data and run with this: python2 test_TADdyn_on_Sox2.py whereas the error logs shows like this: Optimizing 300 particles num scale...
