Streamlining differential exon and 3' UTR analysis

This repository accompanies the diffUTR paper, providing a record of what was done and of the data used. For information about the diffUTR package and its usage, see the package's repository.

Structure

• the results folder contains the results of each method, applied to each dataset.
• the data folder contains some necessary datasets (see about large data files, below).
• the figures folder contains the code used to generate the figures.
• the root directory contains files directly used in the manuscript.

Large data files

Some files were two large to be included here. These include:

• The gencode gene annotation, which should be decompressed and placed in data/large/. It can be downloaded from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.annotation.gtf.gz.
• The raw data and aligned reads for the different datasets used. The reads from the published LTP dataset can be downloaded from the GEO/SRA (GSE84643). The simulated reads can be downloaded from figshare.