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NVIDIA-Genomics-Research / AtacWorks

Deep learning based processing of Atac-seq data
https://clara-parabricks.github.io/AtacWorks/
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tutorial2: Inference output data #188

Closed hugokitano closed 4 years ago

hugokitano commented 4 years ago

Is it possible that we can download the outputs of the Tutorial 2 output? I'd like to take a look at them before I start running a GPU. Thanks!

NK_inferred.track.bedGraph
NK_inferred.track.bw
NK_inferred.peaks.bedGraph.
NK_inferred.peaks.bw

Hugo

avantikalal commented 4 years ago

These files are available here: https://atacworks-paper.s3.us-east-2.amazonaws.com/dsc_atac_blood_cell_denoising_experiments/50_cells/output/NK_inf.wg.peaks.bw https://atacworks-paper.s3.us-east-2.amazonaws.com/dsc_atac_blood_cell_denoising_experiments/50_cells/output/NK_inf.wg.track.bw

However, the peaks.bw file here was created using the alternate inference command in Appendix 1 of the tutorial. So it contains the probability of each base being part of a peak. You can use it to generate peak calls with different probability thresholds using MACS2 as described in the tutorial.