how to create pseudo-replicate files

[songxh1996]

python encode_task_reproducibility.py
liver1_peaks.narrowPeak.gz,liver2_peaks.narrowPeak.gz
--peak-type narrowPeak
--prefix liver_rep
--chrsz genome_nomt.size --out-dir ./
ENCODE DCC reproducibility QC.: error: the following arguments are required: --peaks-pr

Thank you for your resources, I encountered such an error when running the code, I need pseudo-replicate, but in my previous analysis, I did not get it. If I miss important information, any tips from you will help me. In addition, they are necessary in the analysis, right?

[leepc12]

I'm still not sure why you want to run encode_task_reproducibility.py separately.
Yes, they are necessary for the specific analysis encode_task_reproducibility.py.

You can't make pseudo replicated (pr) peak files. Please find those pr narrowPeak.gz files under call-overlap_pr or call-idr_pr directory and feed them to encode_task_reproducibility.py.