Before installing the CracTools, you may want to check out and install CRAC that is the RNA-Seq analysis and mapping software that you will use before running the CracTools pipelines.

Installing the CracTools

The CracTools are set of pipeline that can all be independently installed, however they all rely on the CracTools-core package that contains datastructures, and utilities to help the built of the CracTools pipeline.

CracTools are written in Perl and packaged as CPAN modules wich can be installed easily with cpanm (see CPAN install page).

From CPAN repository

The easiest way to install CracTools-core modules is to use CPAN with the cpan-minus script:

cpanm CracTools-core

This will automatically download all missing dependancies and install all modules under /usr/lib/perl5/. If you want to install the CracTools under a local directory, usr -l local_dir option of cpanm.

From the source code

You can also download the CracTools-core source code tarball and install it with cpanm:

cpanm CracTools-core.tar.gz

Installing a CracTools pipeline

Each CracTools pipeline can be installed the same way as the CracTools-core package by using the source code. Some of them are also availabe on CPAN or upon request.

Using the CracTools

There is many things you can do with the CracTools, either using a dedicated pipeline like ChimCT for detecting chimeric junction. You can also build your own cractool by following this guide.

But let start with a simple extraction task to generate output files holding biological variants (SNVs, Indels, Splices, Chimeras) identified by CRAC in an RNA-Seq sample.

Extracting genomic and transcriptomic variants identified by CRAC using cractools-extract

The CracTools are built on top of CRAC software. Before running the CracTools, you’ll often need to run CRAC on one (or more) RNA-Seq samples an generate a BAM file for each one of them with a command like :

crac -i my-index -k 22 -r reads_1.fastq reads_2.fastq --bam -o crac.bam

You will also need to sort and index the BAM records to enable fast searching of genomic intervals. Samtools propose some tools to do that for you :

samtools view crac.bam | samtools sort - crac-sorted && samtools index crac-sorted.bam

Now you are ready to use the CracTools to extract, annotate and enhanced genomic and transcriptomic variants identified by CRAC. For example you can simply use the tool cractools-extract that is shipped with the CracTools-core package in order to extract and aggregate variant identified at the read scale into a set of files using standard format:

  • VCF file for SNV and Indels variants
  • BED file for splice junctions
  • TSV file for chimeric junctions (since no standard has been accepted yet)

This command will extract all variants identified by CRAC :

cractools-extract crac-sorted.bam --mutations cractools.vcf --splices cractools-splices.bed --chimeras cractools-chimeras.tsv

This is a rapid overview of a Workflow that integrates CRAC and the CracTools, but there is many more things that you can do with the CT. Check-out the available CT pipelines in the “softwares” menu or the developper’s guide to build your own specialized pipeline.