idr
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nboley
IDR
Hi, I'm working with a relatively small number of peaks (~100; which is probably in contrast to most use cases, which will have thousands+), due to a small genome size...
I have downloaded clip_seq data narrow Peak files from ENCODE and am trying to perform IDR directly on them. I call the command: idr --samples rep1.peak rep2.peak -i 0.05 --rank...
Hi, I'm confusing about how to get the reproducible peaks from replicates of histone data. The IDR is recommended in ENCODE pipeline for TF ChIPseq data. How about histone data?...
Hi, I'm hoping I can get some answers even though this github looks pretty deserted. I ran the idr using input files that looks like this: ``` track type=narrowPeak name="peaks1.bed"...
I was running idr on rep1 and rep2 and found out some of the output for rep2 do not match the rep2 narrowPeak file. I'm copying one of the offending...
Thanks for this great tool. We are finding that the value of IDR changes based on the order of peak1 and peak2 in the --samples argument. For example, "--samples peak1...
Hello, I been getting different errors when running IDR. If I run Idr v2.0.2 I get the following error: ./idr --input-file-type bed --rank 7 --plot --verbose --samples peaks_TGATCA_clean.bed peaks_PrNotT_clean.bed Loading...
I got errors when running pipelines for some samples from Butcher's lab. This PR is a fix for it. ``` Traceback (most recent call last): File "/software/miniconda3/envs/bds_atac_py3/bin/idr", line 4, in...
Hello, I am having a weird issue with IDR. I am running the command with 2 .narrowPeak files as input, p.value in `--rank` and `--plot` option on (code below). Another...
Does the program support idr calculation considering more that two samples? When I enter three files for the --samples argument, I get the following error message: **idr: error: unrecognized arguments:...
