Treehouse Comparative Analysis of RNA Expression (CARE) UCSC Treehouse Childhood Cancer Initiative

Documentation on the docker used in the Vaske 2019 comparative tumor RNA-Seq analysis publication is available here.

Treehouse Comparative Analysis of RNA Expression (CARE) is a dockerized pipeline of Jupyter notebooks that performs outlier analysis on an RNA-Seq expression file generated from a FASTQ by the UCSC UCSC Treehouse Toil RNA-Seq expression pipeline, vs a background compendium of samples. It generates two HTML documents summarizing the results that you can populate with your sample's clinical information.

Requirements

Linux
Git
Make
Docker
6.5 Gb of disk space, approximately, for background compendium and reference files
200 Mb disk space per focus sample for combined input+output

Usage

Clone:

git clone https://github.com/UCSC-Treehouse/CARE.git
cd CARE

Checkout the latest release:

git checkout 0.17.1.0

Use Make to run the docker: make run

This will:

• Pull the docker
• Download the background compendium and reference files if not already present. (May take several minutes; compendium download is ~1.5GB).
• Download a test sample
• Run CARE on the test sample

Manual downloads

If you prefer, you can manually download the input tgz files from the following URLs:

• https://xena.treehouse.gi.ucsc.edu/download/CARE/TumorCompendium_v10_PolyA.tgz
• https://xena.treehouse.gi.ucsc.edu/download/CARE/TreehouseReferences-2020-03-30.tgz
• https://xena.treehouse.gi.ucsc.edu/download/CARE/TreehouseExampleFocusSample-TH03_0013_S02-2019-10-23.tgz
• https://xena.treehouse.gi.ucsc.edu/download/CARE/TreehouseExampleManifest-2019-10.24.tgz

MD5sums:

cfafeb5ff7b93591d0a80894061b5f3e  TumorCompendium_v10_PolyA.tgz
9fe4889ab1a69620ce725d47a3decba0  TreehouseReferences-2020-03-30.tgz
4bc8001b744d5ea6a8d9a94db06a7df9  TreehouseExampleFocusSample-TH03_0013_S02-2019-10-23.tgz
03bb977bb9610a19c84e98a788a96d41  TreehouseExampleManifest-2019-10.24.tgz

To use, place them in the "resources" folder as the original tgz archive without extracting.

Documentation

Docs are available here.

Contact

You can open an issue with your question or get in touch via the Treehouse contact form.