-
Notifications
You must be signed in to change notification settings - Fork 79
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
differences between "new" and "old" pipeline #139
Comments
Are you sure you are comparing the same files across the two runs? Can you
provide some details/logs etc. so we can look into it.
They should generate identical or near identical results.
…-Anshul.
On Thu, Sep 6, 2018 at 1:13 PM Bian Li ***@***.***> wrote:
Hi @akundaje <https://github.com/akundaje> @leepc12
<https://github.com/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!
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#139>, or mute
the thread
<https://github.com/notifications/unsubscribe-auth/AAI7EQ8fNdL1hcGji9Ed_N7CKCkLitGMks5uYYHsgaJpZM4WdooD>
.
|
@computbiolgeek Please post your input JSON for the new pipeline and command line for the old one. |
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? |
No, both use the same default idr threshold (0.1).
Please upload your input JSON file.
It seems like you have `"atac.idr_thresh" : 0.05` in it.
Jin
…On Thu, Sep 6, 2018 at 4:41 PM Bian Li ***@***.***> wrote:
Is it likely that it is because the two pipelines are using different
default idr thredhold? The WDL-based uses 0.05 whereas this one uses 0.1?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#139 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AIOd_I8swRwS6A9VKiTw9kQPzmo3q6umks5uYbKngaJpZM4WdooD>
.
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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!
The text was updated successfully, but these errors were encountered: