No description, website, or topics provided.
Clone or download
Latest commit 99183da Nov 27, 2018
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
src Fixes issue #1 Nov 20, 2018
CMakeLists.txt first commit Aug 22, 2018
LICENSE Initial commit Nov 12, 2018
README.md Update README.md Nov 27, 2018

README.md

bustools

bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.

The design and motivation for the BUS format and BUStools are described in detail in

P Melsted, V Ntranos, L Pachter, The Barcode, UMI, Set format and BUStools, bioRxiv 2018 pp: 472571.

BUS format

bustools works with BUS files which can be generated efficiently from raw sequencing data, e.g. using kallisto.

Installation

Download bustools with

git clone https://github.com/BUStools/bustools.git

Move to the bustools directory

cd bustools

Make a build directory and move there:

mkdir build

cd build

Run cmake:

cmake ..

Build the code:

make

The bustools executable is now located in build/src. To install bustools into the cmake install prefix path type:

make install

Usage

To see a list of available commands type bustools in the terminal

> bustools 
Usage: bustools <CMD> [arguments] ..

Where <CMD> can be one of:

sort            Sort bus file by barcodes and UMI
text            Output as tab separated text file

Running bustools <CMD> without arguments prints usage information for <CMD>

Sorting

Raw BUS output from pseudoalignment programs may be unsorted. To simply and accelerate downstream processing BUS files can be sorted using bustools sort

> bustools sort 
Usage: bustools sort [options] bus-files

Options:
-t, --threads         Number of threads to use
-o, --output          File for sorted output

This will create a new BUS file where the BUS records are sorted by barcode first, UMI second, and equivalence class third.

Text

BUS files can be converted to a tab-separated format for easy inspection and processing using shell scripts or high level languages. bustools text

> bustools text
Usage: bustools text [options] bus-files

Options: 
-o, --output          File for text output