- Improved transcript concentration estimates (when compared with Cufflinks and PennSeq)
Repeatable concentration estimates across different library preps
Improved transcript concentration fold-change estimates: more accurate detection of differential expression
Detection and classification of bias types in RNA-Seq data
Mix² runs significantly* faster than Cufflinks!
Correlation between qPCR and FPKM fold changes between UHR and HBR for the Mix² vs Cufflinks, and ROC for a classification experiment. The Mix² model achieves the best correlation whereas Cufflinks yields significant amount of transcripts whose FPKM fold change lies considerably above or below the majority of FPKM fold changes and is treated as not detected.
* Contact info(at)lexogen.com for more information.
Mix², a new algorithm for accurate quantification of transcript isoforms in RNA-Seq data
Fragment bias in RNA-Seq poses a serious challenge to the accurate quantification of gene isoforms. The novel Mix² algorithm makes no assumption about fragment bias but fits a mixture model to the data, thus inferring the bias automatically. Mix² model leads to considerably better correlation between known and estimated transcript isoform concentration than Cufflinks and PennSeq, which results in substantially increased accuracy in the detection of differential expression. Further details can be found in the manuscript on BioRxiv.
Application and participation
Applications should be completed by January 31 through the following web page Application form
All applicants will be given a stand-alone executable of the Mix² software for free use on their own RNA-Seq data.
We ask the participants to submit reports in free format including results generated with the Mix² software. The emphasis of these reports should be on the comparison with their previous algorithms.
The most comprehensive reports will be rewarded with the following prizes.
1st place (1 person) : Mac Book Air (11 inch, Intel Core i5, 125Gb)
2nd places (2 people) : iPad Mini 2 Retina (16Gb, Wifi)
Lexogen is a company based in Vienna, Austria. We provide researchers with innovative solutions for transcriptome analysis. Reliable, user-friendly and affordable protocols that yield reproducible high-quality data are our main focus. Our product portfolio includes RNA-Seq library prep kits*, full-length cDNA amplification kit and other molecular biology products.
*RNA-Seq library prep starts at as low as 19 EUR (26 USD) per sample.