gaheens/gdc-rnaseq-tool

Tool to download/merge RNASeq data from the GDC Portal in matrices identified by TCGA barcode

gdc-rnaseq-tool

Tool to download / merge individual RNASeq files from the GDC Portal into a matrices identified by TCGA barcode.

Inputs and Outputs:

I/O	File
Input	GDC Manifest File
Output	Merged_Counts.tsv (HTSeq - Counts)
	Merged_FPKM.tsv (HTSeq - FPKM)
	Merged_FPKM-UQ.tsv (HTSeq - FPKM-UQ)
	Merged_miRNA_Counts.tsv
	Merged_miRNA_rpmm.tsv

Bioinformatics Pipeline Information:

RNA-Seq Pipeline

miRNA-Seq Pipeline

Requirements:

• Python 3+
• pandas ( https://pandas.pydata.org/pandas-docs/stable/install.html ): pip3 install pandas

Quick Start:

1. Download gdc-rnaseq-tool.py python script
2. Download manifest containing RNA/miRNA expression files from https://portal.gdc.cancer.gov/
3. python3 gdc-rnaseq-tool.py <manifest_file>

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The GDC RNASeq tool produces matrices of merged RNA/MiRNA expression data given a manifest file.

Usage: python3 gdc-rnaseq-tool.py <manifest_file>

Notes:

• A test manifest is provided for troubleshooting: python3 gdc-rnaseq-tool.py Test_Manifest.txt
• Files are by default downloaded to the same folder as the manifest file that was provided

Release Notes:

Version 1.0: Feb 8, 2018

• Initial release

Known Issues: N/A