david-castillo

Hi, That seems correct. Is assembly.fasta what you used to generate the index? genome_seq is a parameter in the inner function doing the parse. That means TADbit fails to process...

If fasta file is correct and you are using conda, can you send me your configuration (conda env export > environment. yml)? David

Hi, After the mapping all the produced files should have the same format, so using hisat2 should not affect the parsing. I tried with your conda environment and had no...

Hi Lucía, I would first try to run the command with the default parameters. `eigenvectors = hic_data.find_compartments()` If you still get the error I recommend you to update your TADbit...

Hi, Yes, that seems to be an issue with the R script. TADbit calls internally this script: `Rscript --vanilla normalize_oneD.R input.csv` so, I'd first check that from R you can...

Hi, Then, it's maybe that the R version called from python is not the correct one if you have multiple installations. You can try to do: `python -c 'from subprocess...

Hello, Can you post the error message that you are having? Regards David

Hi, For a squared matrix just provide the path with --input_matrix as you said. Have a look here http://3dgenomes.github.io/TADbit/tutorial/tutorial_10-Modeling_parameters_optimization.html to understand the parameters. Depending on the resolution modelling a full...

Hi Juan, My bet is that it comes from the same issue. Can you paste the code that you use for the api so I can confirm it's the same...

Hi, gem-mappability comes with gem version 2, verify that the index is built with the same version and not with more recent versions of gem. Is all I can guess...