GSE120104 Processing Pipeline

ChIP-Seq code_examples 5 steps

Publication

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.

Cell (2019) — PMID 31251911

Dataset

GSE120104

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq]

Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.

Processing Steps

Generate Jupyter Notebook
  1. 1

    ChIP-seq data were processed in accordance with ENCODE uniform transcription factor ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/transcription_factor/).

    ChIP-seq
  2. 2

    Briefly, ChIP-seq reads were aligned to the GRCh37 human genome using BWA

    BWA
  3. 3

    PCR duplicates and reads of low quality were filtered

  4. 4

    Peak-calling was performed with SPP and IDR with 0.02 IDR threshhold

    IDR v0.02
  5. 5

    Signal tracks were generated with MACS2 and bigWig applications from UCSC genome browser (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)

    MACS2

Tools Used

ChIP-seq
Raw Source Text 
ChIP-seq data were processed in accordance with ENCODE uniform transcription factor ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/transcription_factor/).
Briefly, ChIP-seq reads were aligned to the GRCh37 human genome using BWA;
PCR duplicates and reads of low quality were filtered;
Peak-calling was performed with SPP and IDR with 0.02 IDR threshhold;
Signal tracks were generated with MACS2 and bigWig applications from UCSC genome browser (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Peak files were narrowPeak files generated by SPP; column information of narrowPeak file is explicated at the link (https://genome-euro.ucsc.edu/FAQ/FAQformat.html#format12).
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