GSE120105 Processing Pipeline

OTHER code_examples 5 steps

Publication

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

Cell (2019) — PMID 31251911

Dataset

GSE120105

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [GRO-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

    Library strategy: GRO-seq

  2. 2

    GRO-seq reads were mapped on the human reference genome using the Bowtie2 local model

    Bowtie2
  3. 3

    Non-redundant reads were determined and kept for downstream analysis by using Samtools

    samtools
  4. 4

    DEseq2 package was used to search for differentially expressed genes (DEGs), which was defined with the following cutoff: adjusted p-value of ≤0.05 and fold change of ≤2/3 or ≥3/2.

    DESeq2
  5. 5

    processed data files format and content: BED and BigWig

    UCSC tools

Tools Used

Bowtie2 DESeq2 UCSC tools
Raw Source Text 
Library strategy: GRO-seq
GRO-seq reads were mapped on the human reference genome using the Bowtie2 local model
Non-redundant reads were determined and kept for downstream analysis by using Samtools
DEseq2 package was used to search for differentially expressed genes (DEGs), which was defined with the following cutoff: adjusted p-value of ≤0.05 and fold change of ≤2/3 or ≥3/2.
Genome_build: GRCh37 (hg19)
processed data files format and content: BED and BigWig
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