Understanding Chip-seq data (ENCODE and other resources)

Understanding Chip-seq data (ENCODE and other resources)

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Hello, I am a beginner in understanding Chip-seq data analysis and just got introduced to Chip-seq data by studying the ENCODE portal documentation (www.encodeproject.org/data-standards/terms/#concordance). I am focusing on Chip-seq for transcription factors. Although, I still have some question such as:

  1. Why each experiment includes ideally two biological replicates?
  2. How should I choose one BigBed file by experiment (among signal IDR thresholded peaks, conservative IDR thresholded peaks, optimal IDR thresholded peaks)?

Thank you! Also, any beginner-friendly resource recommendation for Chip-seq is very welcome.


transcription


encode


factors


chip-seq


replicates

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