AtacWorks

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Error running atacworks train

2

Hi there, I'm running atacworks on some Drosophila ATAC-seq data we had generated, and it's throwing an error at me! atacworks train \ --noisybw ClkZT14_2.sort.bam.cutsites.smoothed_100.coverage.bw \ --cleanbw ClkZT14_1.sort.bam.cutsites.smoothed_100.coverage.bw \ --cleanpeakfile...

albertdyu

Tutorial 1 is recursive?

1

Clicking on "documentation" in this page: https://clara-parabricks.github.io/AtacWorks/tutorials/tutorial1.html Just takes you back to the same page. I can't seem to find any instructions on how to train a model. Apologies if...

albertdyu

Hello, I'm trying to run the example in [tutorial 2](https://github.com/clara-parabricks/AtacWorks/blob/dev-v0.4.0/tutorials/tutorial2.ipynb). I downloaded the files and ran the exact command listed in the tutorial to denoise, but I always got `ConnectionResetError:...

hhvu0102

Removing hard-set versions from requirements.txt to be more compatible with RAPIDS

2

I'm currently updating the `rapids-single-cell-examples` repository to use RAPIDS 21.08 but the firm versions in the atacworks python package are causing numerous conflicts with the rest of the packages in...

cjnolet

error message needing help

1

Hi, Could I run my code like this? Do you see any problems? I mean for the weights_path, could it be my own big.wig of a clean sample? But, when...

elffairy90

[gpuCI] Forward-merge master to dev-v0.4.0

1

Forward-merge triggered by push to `master` that creates a PR to keep `dev-v0.4.0` up-to-date. If this PR is unable to be immediately merged due to conflicts, it will remain open...

GPUtester

Pretrained model for bulk low-quality data

6

Hi @avantikalal, in cases where noisy samples have coverage >= that of the clean samples, should users _always_ forego training and use your pretrained model, nvidia:atac_bulk_lowqual_20m_20m? For example:  If...

avantikalal

Atacworks stuck at "waiting for writter to finish..."

3

Hello, Great paper and great tool and thank you to sharing your docker environment to facilitate the use of your tool, Maybe i'm doing something wrong, but when i'm trying...

rochevin

What does the 6 kb mean?

3

Hello, In the paper, you mentioned, "The network makes predictions for each base in the genome based on coverage values from a surrounding region spanning several kilobases `6kb for the...

YichaoOU

error in pip install -r requirments.txt

1

Hi, I got the following error when doing this step, wondering if I could get help here. THank you! cd AtacWorks && pip install -r requirements.txt ![Screen Shot 2021-03-21 at...

elffairy90