Supplementary Data for MOCCASIN: A method for correcting known and unknown confounders in RNA-Seq-based splicing analysis

Contents

moccasin_paper_env.yaml: conda environment file with R and Python packages and modules needed to reproduce  analyses.

FigureReproduction.zip: data and code to reproduce main and supplemental figures.

MOCCASIN_ExampleDataset.zip: A small subset of the simulated data with example code to run MOCCASIN.

encode_corrected.zip: Folder with batch-corrected ENCODE differential splicing quantifications (dPSI).

(1) moccasin_paper_env.yaml

Use the moccasin_paper_env.yaml file to create a conda environment from which all analyses for the paper can be reproduced.

# need to first install conda. See here:
# https://docs.conda.io/en/latest/miniconda.html
# Next, create a conda environment:
conda env create --name moccasin_paper_env --file moccasin_paper_env.yaml --force
# Activate the environment:
conda activate moccasin_paper_env

The only Python packages not included in this environment are MAJIQ & VOILA. Please see majiq.biocipers.org for installation instructions.

(2) FigureReproduction.zip

Within FigureReproduction are folders with code and data to reproduce the main and supplemental figures of the publication. Each folder contains data, script(s) and a README.txt with instructions on how to reproduce figures.

(3) MOCCASIN_ExampleDataset.zip

Within this folder is an example dataset to test MOCCASIN. The README.txt file contains detailed line-by-line instructions for how to run MOCCASIN and do post-MOCCASIN analyses. In this example, we show how to run MOCCASIN on a group of .majiq samples with one known confounding effect. Also demonstrated is how to run an "explore unknown residuals" analysis as described in the detailed methods in the supplemental of the paper. 

(4) encode_corrected.zip

Includes a file called ENCODE_BeforeAndAfterMOCCASIN.voila.tsv.zip which includes LSV quantifications before and after MOCCASIN. Each row in the file represents a junction from an LSV. Each column header starts with the prefix "BeforeMOCCASIN" or "AfterMOCCASIN" and headers ending in dPSI corresponds to the dPSI of an ENCODE knockdown vs control experiment.