Re: IDR considering non-overlapping peaks

[Anshul Kundaje]

Hmm .. this shouldn't be happening. Can you share your Oracle and biorep peak files so we can look into it further.

Thanks

Anshul

On Mon, Mar 18, 2019, 12:29 PM <l...@ucdavis.edu> wrote:

Hello,

I've been using IDR for TF ChIP-Seq analysis, and I've been pretty satisfied with the ability of IDR to identify reproducible and consistent peaks between biological replicates.

My brief understanding of IDR logic is that if a peak list is provided, IDR would identify all overlapping peaks in both bioreps and evaluate their reproducibility based on signal. Therefore, if a peak in the oracle peak file does not have a respective overlapping peak in both bioreps, it will be excluded from the final IDR list. 

However, there are some instances that IDR is considering peaks that are not present in one of the bioreps (see peak B in the example bellow). 

The code that I use for the analysis was the following:

idr --samples biorep1.peak.narrowPeak biorep2.peak.narrowPeak --peak-list oracle.peaks

Can someone please explain me why this is happening? Am I missing something with the logic?

Thank you very much for the help,

Best,

Leonardo

--
You received this message because you are subscribed to the Google Groups "idr-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to idr-discuss...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[l...@ucdavis.edu]

Dear Anshul Kundaje,

Thank you for reaching out,

I'm uploading the following files:

oracle.peaks.narrowPeak

biorep1.peaks.narrowPeak

biorep2.peaks.narrowPeak

idr.output.bed

https://drive.google.com/drive/folders/14meKxGkCGzng3Lj9m-dKyVEANElBa75c?usp=sharing

 Some examples of the problem can be found in peak 8519 and peak 4836 in the oracle.

The code I used to generate the idr.output.bed was:

idr --samples biorep1.peaks.narrowPeak biorep2.peaks.narrowPeak --peak-list oracle.peaks.narrowPeak --idr-threshold 0.01 --plot --output-file idr.output.bed 

Please let me know your comments.