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differences between "new" and "old" pipeline #139

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computbiolgeek opened this issue Sep 6, 2018 · 4 comments
Open

differences between "new" and "old" pipeline #139

computbiolgeek opened this issue Sep 6, 2018 · 4 comments

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@computbiolgeek
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Hi @akundaje @leepc12 , I noticed that the README was updated like an hour ago, which basically says that the WDL-based pipeline is an exact copy of this pipeline. However, what I found was that using the WDL-based pipeline reduced significantly the number of idr-thresholded peaks. For example, for the ATAC-seq experiment ENCSR668VCT, the WDL-based pipeline produced 103385 peaks, whereas, this pipeline produced 146794 peaks. What should we be concerned about here? Thank you!

@akundaje
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akundaje commented Sep 6, 2018 via email

@leepc12
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leepc12 commented Sep 6, 2018

@computbiolgeek Please post your input JSON for the new pipeline and command line for the old one.

@computbiolgeek
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computbiolgeek commented Sep 6, 2018

Is it likely that it is because the two pipelines are using different default idr thresholds? The WDL-based uses 0.05 whereas this one uses 0.1?

@leepc12
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leepc12 commented Sep 7, 2018 via email

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