idr-discuss

Contact owners and managers

1–30 of 123

Welcome to the discussion group for users and developers of the Irreproducible Discovery Rate (IDR) statistical framework used to threshold and analyze reproducibility of quantitative biological experiments such as ChIP-seq data.

IDR was used extensively in the analysis of ChIP-seq data from the ENCODE (Encyclopedia of DNA elements) consortium. It is part of the official ENCODE/modENCODE data standards.

The statistcal method was developed by Qunhua Li, Ben Brown, Haiyan Huang and Peter Bickel at U.C. Berkeley. See http://projecteuclid.org/euclid.aoas/1318514284 for the publication in Annals of Applied Statistics (Li et al. 2011) introducing the statistical framework. For an intuitive description of the IDR method and a description of the various plots generated by the IDR package read this IDR-101 document compiled by Qunhua Li.

The method was further adapted, tweaked and deployed for systematic analysis of ChIP-seq data by Anshul Kundaje and others as part of the ENCODE consortium.

A manuscript detailing practical aspects of the IDR pipeline is in the works. A beta version of the pipeline is available at https://sites.google.com/site/anshulkundaje/projects/idr

0 selected

erfan sharifi, Anshul Kundaje3

4/30/22

Pooled Peak List

Thanks for your respond! the other things that is a little bit strange is that when I run the idr

unread,

Pooled Peak List

Thanks for your respond! the other things that is a little bit strange is that when I run the idr

4/30/22

Sumit Paliwal, … Ivan Molineris5

12/4/20

idr for RNA-Sequencing data

Dear Anshul, can you please elaborate a bit about the assumption that RNA expression violates? I'

unread,

idr for RNA-Sequencing data

Dear Anshul, can you please elaborate a bit about the assumption that RNA expression violates? I'

12/4/20

Frédéric Crémazy, Anshul Kundaje2

10/29/20

IDR problem with ChIPmentation data

We don't recommend using IDR with histone marks and MACS2 as the peak caller. Instead just use

unread,

IDR problem with ChIPmentation data

We don't recommend using IDR with histone marks and MACS2 as the peak caller. Instead just use

10/29/20

laij...@gmail.com

10/15/20

Length of peaks

Hello, I used MACS2 to obtain .narrowPeak files for 2 biological replicates to use as input to IDR. I

unread,

Length of peaks

Hello, I used MACS2 to obtain .narrowPeak files for 2 biological replicates to use as input to IDR. I

10/15/20

10/14/20

ChIP-Seq pipeline in "tf" mode

Hello, The goal of running ChIP-Seq pipeline for me was to figure out the binding regions of BZW1, HA

unread,

ChIP-Seq pipeline in "tf" mode

Hello, The goal of running ChIP-Seq pipeline for me was to figure out the binding regions of BZW1, HA

10/14/20

Lucy, … Anshul Kundaje4

10/12/20

IDR threshold - 0.1 or 0.05?

https://github.com/kundajelab/idr Please read the file format carefully. Column 12 is globalIDR float

unread,

IDR threshold - 0.1 or 0.05?

https://github.com/kundajelab/idr Please read the file format carefully. Column 12 is globalIDR float

10/12/20

9/21/20

Integrating IDR into NGS pipelines

Hello, I am wondering if it is possible to integrate idr into a NGS pipeline, more specifically ChIP-

unread,

Integrating IDR into NGS pipelines

Hello, I am wondering if it is possible to integrate idr into a NGS pipeline, more specifically ChIP-

9/21/20

Emi Ling, Georgi Marinov3

3/17/20

IDR on CUT&RUN data

Thank you! I will give it a try. On Sunday, March 1, 2020 at 5:11:25 PM UTC-5, Georgi Marinov wrote:

unread,

IDR on CUT&RUN data

Thank you! I will give it a try. On Sunday, March 1, 2020 at 5:11:25 PM UTC-5, Georgi Marinov wrote:

3/17/20

Bahareh Haddad Derafshi, Anshul Kundaje3

12/18/19

Bam input generated seperatly-cannot run the bds

On Wednesday, December 18, 2019 at 8:01:01 AM UTC-8, Anshul Kundaje wrote: The BDS pipelines have

unread,

Bam input generated seperatly-cannot run the bds

On Wednesday, December 18, 2019 at 8:01:01 AM UTC-8, Anshul Kundaje wrote: The BDS pipelines have

12/18/19

Anshul Kundaje, l...@ucdavis.edu2

3/22/19

Re: IDR considering non-overlapping peaks

Dear Anshul Kundaje, Thank you for reaching out, I'm uploading the following files: oracle.peaks.

unread,

Re: IDR considering non-overlapping peaks

Dear Anshul Kundaje, Thank you for reaching out, I'm uploading the following files: oracle.peaks.

3/22/19

l...@ucdavis.edu

3/18/19

Question about why non-overlapping peaks are being called reproducible

Hello, I've been using IDR for TF ChIP-Seq analysis, and I've been pretty satisfied with the

unread,

Question about why non-overlapping peaks are being called reproducible

Hello, I've been using IDR for TF ChIP-Seq analysis, and I've been pretty satisfied with the

3/18/19

aimin....@gmail.com, Anshul Kundaje2

1/17/19

object 'tag.lwcc' not found error when call peaks from run_spp.R

Yes it can break if you switch your R version. I would recommend sticking to our complete pipeline

unread,

object 'tag.lwcc' not found error when call peaks from run_spp.R

Yes it can break if you switch your R version. I would recommend sticking to our complete pipeline

1/17/19

Lucy, … Mariangela4

1/10/19

Should I filter MACS2 peaks before IDR?

Hi Anshul, Can I be confident by using the MACS2 output obtained with the following line for the next

unread,

Should I filter MACS2 peaks before IDR?

Hi Anshul, Can I be confident by using the MACS2 output obtained with the following line for the next

1/10/19

12/7/18

Estimation of the fold enrichment value when running IDR with pvalue as ranking measure

Hi, I performed IDR analysis on MACS2 peaks with the ` pvalue ` as ranking measure idr --samples ${

unread,

Estimation of the fold enrichment value when running IDR with pvalue as ranking measure

Hi, I performed IDR analysis on MACS2 peaks with the ` pvalue ` as ranking measure idr --samples ${

12/7/18

9/23/18

--use-best-multisummit-IDR

Hi, As I performed peakcalling with MACS2 callpeak and the --call-summits option, I was wondering

unread,

--use-best-multisummit-IDR

Hi, As I performed peakcalling with MACS2 callpeak and the --call-summits option, I was wondering

9/23/18

Lucy, Anshul Kundaje2

9/13/18

Correspondence curves

Yes. https://github.com/kundajelab/idr Anshul On Thu, Sep 13, 2018, 9:11 AM Lucy <lucycgarner@

unread,

Correspondence curves

Yes. https://github.com/kundajelab/idr Anshul On Thu, Sep 13, 2018, 9:11 AM Lucy <lucycgarner@

9/13/18

Lucy, Anshul Kundaje4

9/13/18

Peak summits after IDR analysis

bedtools intersect -wa -wb -a merged.bed -b sampleApeaks.bed sampleBpeaks.bed On Thu, Sep 13, 2018, 5

unread,

Peak summits after IDR analysis

bedtools intersect -wa -wb -a merged.bed -b sampleApeaks.bed sampleBpeaks.bed On Thu, Sep 13, 2018, 5

9/13/18

WeiSheng Zheng, Jin2

7/10/18

idr-v2.0.2/2.0.3 running error

Did you have cython installed on your system? If so the following command should work. python -c

unread,

idr-v2.0.2/2.0.3 running error

Did you have cython installed on your system? If so the following command should work. python -c

7/10/18

rt...@nyu.edu, … Jin6

6/19/18

Could not install spp

This looks a complicated dependency problem and it's very hard to debug. I recommend to use our

unread,

Could not install spp

This looks a complicated dependency problem and it's very hard to debug. I recommend to use our

6/19/18

Yan Zhu, Anshul Kundaje4

2/16/18

construct ROC from SPP/idr/conservative set

No the signal value is ChIP - input with a penalty for peak shape (You'll have to look at the

unread,

construct ROC from SPP/idr/conservative set

No the signal value is ChIP - input with a penalty for peak shape (You'll have to look at the

2/16/18

Toni Paternina, Jin6

2/12/18

Bug when using --use-nonoverlapping-peaks option

Thanks! Please let us know the result then I will make a hot fix for it based on your implementation.

unread,

Bug when using --use-nonoverlapping-peaks option

Thanks! Please let us know the result then I will make a hot fix for it based on your implementation.

2/12/18

洪彧丞, Jin2

2/7/18

Questions about columns definitions of AQUAS output

1. Output column description is here https://github.com/kundajelab/idr#output. 2. IDR keeps strand

unread,

Questions about columns definitions of AQUAS output

1. Output column description is here https://github.com/kundajelab/idr#output. 2. IDR keeps strand

2/7/18

Chun, Anshul Kundaje2

1/26/18

Does higher IDR mean less 'reproducible' or vice versa?

IDR package produces a output file which mimics the input narrowPeak file with additional two columns

unread,

Does higher IDR mean less 'reproducible' or vice versa?

IDR package produces a output file which mimics the input narrowPeak file with additional two columns

1/26/18

洪彧丞, … Jin17

12/30/17

Question about AQUAS pipeline ( the version of AQUAS pipeline is download at 2017/02/17)

Yes `-type histone` or just `-histone` should work. Jin On Fri, Dec 29, 2017 at 1:48 AM, 洪彧丞 <

unread,

Question about AQUAS pipeline ( the version of AQUAS pipeline is download at 2017/02/17)

Yes `-type histone` or just `-histone` should work. Jin On Fri, Dec 29, 2017 at 1:48 AM, 洪彧丞 <

12/30/17

11/30/17

Hello Xi Wang, Yes, this is MACS2 issue. We already knew about this so our latest version of the

unread,

Hello Xi Wang, Yes, this is MACS2 issue. We already knew about this so our latest version of the

11/30/17

Sammy Klasfeld, Anshul Kundaje5

10/3/17

Pseudo-Pooled Replicates

Also our most common use case is 2 reps. Anshul. On Oct 2, 2017 9:48 PM, "Anshul Kundaje"

unread,

Pseudo-Pooled Replicates

Also our most common use case is 2 reps. Anshul. On Oct 2, 2017 9:48 PM, "Anshul Kundaje"

10/3/17

came...@cardiff.ac.uk, Anshul Kundaje3

9/8/17

IDR - Pooled Peak files

That makes sense. I'll pool all 4 replicates for my IDR Analysis. Many Thanks Anshul, for the

unread,

IDR - Pooled Peak files

That makes sense. I'll pool all 4 replicates for my IDR Analysis. Many Thanks Anshul, for the

9/8/17

Paul Finn, Anshul Kundaje7

8/30/17

Low peak call for spp-IDR peak calling

Also worth running this data through Macs2 + IDR using the same procedure. If your TF has more

unread,

Low peak call for spp-IDR peak calling

Also worth running this data through Macs2 + IDR using the same procedure. If your TF has more

8/30/17

Ajeet Mandal, Jin3

8/3/17

Unable to install SPP on Linux.

Thanks Jin for the github link. - Ajeet On Friday, July 21, 2017 at 6:51:26 PM UTC-4, Ajeet Mandal

unread,

Unable to install SPP on Linux.

Thanks Jin for the github link. - Ajeet On Friday, July 21, 2017 at 6:51:26 PM UTC-4, Ajeet Mandal

8/3/17

kiran girdhar, Anshul Kundaje11

7/25/17

IDR analysis on 100 different peak files

You can try it on your data itself with IDR and with just naive overlap. The rank-rank IDR plots will

unread,

IDR analysis on 100 different peak files

You can try it on your data itself with IDR and with just naive overlap. The rank-rank IDR plots will

7/25/17

Search

Clear search

Close search

Google apps

Main menu