Bootstrap Estimation Tool for RNA-Seq

pip install BENTO-Seq


This directory contains the bootstrap tool to estimate PSI distributions based on aligned RNA-Seq data (BAM files). The RNAseq data must be provided as a binary, sorted, and indexed BAM file.Before using the package, symlink it using:

python develop

or install it globally using:

python install

The basic usage of the script is:

bento-seq event_definitions bamfile output_file [OPTIONS]

Two sample BAM files (TopHat2_chr21.bam and STAR_chr21.bam) and a sample event specfication file ( are provided in the examples/ folder to test the bootstrap tool.

We are providing a number of genomewide sets of alternative splicing events for human (hg19, hg39) and mouse (mm9, mm10) which are downloaded automatically when first used. To use them, simply use the name of the genome assembly in place of event_definitions, e.g.:

bento-seq hg19 examples/STAR_chr21.bam examples_chr21_STAR.results

If you already have a a set of alternative splicing events that you would like to use, provide the path to the event definitions instead:

bento-seq examples/ examples/STAR_chr21.bam examples/events_chr21_STAR.results

BENTO-Seq supports bam-files created with STAR or TopHat and BENTO-Seq will automatically detect which kind of file you provided. E.g. to run the same task with a TopHat bam-file:

bento-seq examples/ examples/TopHat2_chr21.bam examples/events_chr21_TopHat.results

There are a number of other command line options. Run:

bento-seq -h

to get an explanation on their usage.