Call for Early Access Program of Mix-Square algorithm for RNA-Seq analysis

Mix-Square is a software tool for the accurate quantification of transcript isoforms for RNA-Seq data generated from NGS

Lexogen is seeking participants for an early access program for this novel algorithm

Mix-Square, a new algorithm for accurate RNA-seq data analysis

Fragment bias in RNA-Seq poses a serious challenge to the accurate quantification of gene isoforms. The novel Mix-Square algorithm makes no assumptions about fragment bias but fits a mixture model to the data, thus inferring the bias automatically. This yields more accurate abundance estimates and can further be used to investigate the types of positional bias present in RNA-Seq data. On publicly available RNA-Seq test sets Lexogen showed that the Mix-Square model leads to considerably better correlation between known and estimated isoform concentration than Cufflinks and PennSeq. This, in turn, results in substantially increased accuracy in the detection of differential expression (further details can be found in the manuscript


Lexogen is looking for applicants for this program. Applications should be completed by January 18th through the following web page:


Lexogen will review the applications, and select 50 participants. These participants will be given a stand-alone executable of the Mix-Square software for free use on their own RNA-Seq data.

Reports and Prizes

We ask participants to submit reports in free format including results generated with the Mix-Square 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 : MacBook Air 11 inch, Intel Core i5, 128Gb, one person
2nd and 3rd places : iPad Mini 2 Retina, 16Gb Wifi

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