Tool to download / merge individual RNASeq files from the GDC Portal into a matrices identified by TCGA barcode.
Description:
The gdc-rnaseq-tool
performs the following:
The script will ignore any files in the manifest file that are not Transcriptome Profiling files generated from the GDC RNA-Seq / miRNA-Seq bioinformatics pipelines located on the GDC Main Portal:
RNA-Seq Bioinformatics Pipeline Documentation
miRNA-Seq Bioinformatics Pipeline Documentation
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 |
Requirements:
pip3 install pandas
pip3 install requests
Quick Start:
gdc-rnaseq-tool.py
python scriptpython3 gdc-rnaseq-tool.py <manifest_file>
Optional: Add --hugo
to the command to include the HUGO gene symbol as a separate column.
python3 gdc-rnaseq-tool.py <manifest_file> --hugo
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:
python3 gdc-rnaseq-tool.py Test_Manifest.txt
Release Notes:
Version 1.0: Feb 8, 2018
Known Issues: N/A