CRAC is the only RNA-Seq mapping software that include the discovery of transcriptomic and genomic variants like splice junction, chimeric junction, SNVs, Indels in a single analysis step using a built-in error detection method enabling high precison and sensitivity.
Find more about CRAC's concept here.
Mucaki et al published an article in BMC Medical Genomics entitled “A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer”.
Their pipeline uses both CRAC and Casava for the sequence alignment, then SNVs and indels were called using GATK. There is little agreement between both methods and the authors exhibit an example of a discordance, which is at CRAC’s advantage.
Several users had the same issue, with
You may not have the good version of this library. You should install
libhts1, which doesn’t seem to be directly available under Ubuntu 14.04.
You can find more details on that issue in the FAQ.
If you love CRAC and you want to get the most out of it, take a look at the new version of the CracTools that is a complete toolbox designed to build pipelines (in Perl) on top of CRAC.
It is also shipped with a command-line tool that extracts splicing variants, chimeric variants, indels and SNPs identified by CRAC at the read level then collapses them into standard formats (BED,VCF).
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New releases and related tools will be announced through the CRAC mailing list.
Check out the CracTools : Integrated pipelines for RNA-Seq analysis using CRAC additional fields, annotation and much more.
A galaxy wrapper for CRAC is available and can be downloaded here.
Any question regarding the software? Send an email to firstname.lastname@example.org.
A question, a comment, a remark on the algorithm or the article, send an email to email@example.com
Nicolas Philippe, Mikaël Salson, Thérèse Commes and Eric Rivals.CRAC: an integrated approach to the analysis of RNA-seq reads doi:10.1186/gb-2013-14-3-r30