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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
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how to create pseudo-replicate files #299

Open songxh1996 opened 9 months ago

songxh1996 commented 9 months ago

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 commented 7 months ago

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.