TRNanalysis (Transcriptional Regulatory Networks analysis)

Pipelines and test datasets for TRNs analysis using ChIP-exo and RNA-seq dataset

The pipelines and test datasets provided here are designed for researchers who want to analyze TRNs using ChIP-exo and RNA-seq data. The information of files provided are described below:

Pipelines : Download .ipynb file (for Google Colab or Jupyter notebook)

 - Protocol-A.4_Classification_of_Regulatory_Roles.ipynb : Python-based automated pipeline for classifying the regulatory roles of each curated peak from ChIP-exo datasets.
 - Protocol-B.1_Data_Pre-processing_for_RNA-seq_Dataset.ipynb : Python-based pipeline for preprocessing of RNA-seq datasets.
 - Protocol-B.2_Calculation_of_Differentially_Expressed_Genes.ipynb : R-based pipeline for calculating the DEGs using DESeq2.
  Using Colab in local runtime : https://research.google.com/colaboratory/local-runtimes.html
  Using RNA-seq pipeline in Colab : https://drive.google.com/drive/folders/15GbmfyVQtEht3zDOkjJKDZ26NVwgux4W?usp=sharing

Test datasets : Download the files to your working directory

 - ChIP-exo dataset : Duplicates of mini_ChIP-exo-Ecoli-rpoS-mid-37.fastq.gz (Only R1 file)
 - RNA-seq dataset
    Control samples : Duplicates of mini_RNA-seq_Ecoli_mid-37.fastq.gz (including R1 and R2 files)
    Experimental samples : Duplicates of mini_RNA-seq_Ecoli_del_rpoS_mid-37.fastq.gz (including R1 and R2 files)
 - Others : GenBank, examples of datasheets, curated peak file, etc.