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3DGenomes / TADbit

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 matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
GNU General Public License v3.0
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Error of TADbit clean #389

Open iagomaceda opened 1 year ago

iagomaceda commented 1 year ago

Hi,

If the user merges 3 or more replicates into a single one using tadbit merge and wants to clean the final folder (to only have the bam file that results from the last merge), the original folders will be deleted.

Example of the code used:

tadbit merge --workdir merge_dir --workdir1 rep1_dir --workdir2 rep2_dir --cpus 16 --skip_comparison [jobid 1]

tadbit merge --workdir merge_dir --workdir1 merge_dir --workdir2 rep3_dir --cpus 16 --skip_comparison [jobid 2]

tadbit clean -w merge_dir -j 1 --delete

When running the tadbit clean command rep1_dir and rep2_dir will be deleted.

TADbit version: 1.0.1 (installed via conda)

Thanks

fransua commented 1 year ago

Hola Iago, can you try the same creating a new workdir for each merge

iagomaceda commented 1 year ago

Hi,

Thanks for the rapid response, fransua.

So the code would be something like this?

tadbit merge --workdir merge_dir_1 --workdir1 rep1_dir --workdir2 rep2_dir --cpus 16 --skip_comparison

tadbit merge --workdir merge_dir_2 --workdir1 merge_dir --workdir2 rep3_dir --cpus 16 --skip_comparison

rm -rf merge_dir_1

Thanks

fransua commented 1 year ago

yes, this should work. (don;t delete before checking... and perhaps you should have a look at the comparisons. To make them faster set a low resolution, like 500k or so)

"important bug"... 🤬