The FLUX CAPACITOR

[…] sion 2.02 (ref. ) under default options for paired-end read mapping. Mapped reads were used to quantify transcripts from the Ensembl version 73 gene annotation data set (http://www.ensembl.org) using the Flux Capacitor approach. This strategy deconvolutes reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations, and thus specifically assigns some re […]

[…] the mRNA quantification was calculated at different levels. For exon quantification, overlapping exons of a gene were first merged into meta-exons. Transcripts and splice junctions were quantified by the Flux Capacitor approach []. Gene quantification was calculated as the sum of all transcript RPKMs (reads per kilobase per million) for each gene. Before eQTL analysis, expression quantifications w […]

[…] etermined applying the procedure described above for homology-based prediction to the 12 plant genomes using all bean transcript models as templates. lncRNA transcript expressions were obtained using the Flux Capacitor []. […]

[…] tly, it should be mentioned that several recent publications of islet transcriptomics data do not report on a faulty INS-IGF2 expression as they specifically handle this issue. Eizirik et al. [] used the Flux Capacitor approach [] to specifically handle the problem of reads mapping to exonic regions shared by multiple transcripts. Moran et al. [] addressed the multiple transcript mapping issue by […]

[…] database () version 70 for transcripts assembly using the novel transcripts discovery options. Transcript quantification from the mapped reads and the newly assembled transcripts was performed using the Flux Capacitor approach developed by one of us (M.S.) (http://flux. sammeth.net, ()). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units (‘reads per ki […]

[…] number of mapped RNA-PET 5' tags in the experiment. For RNA-Seq experiments, we used GENCODE v7 transcript expression as measured by RPKM (reads per kilobase per million mapped reads; computed using the flux capacitor []) to measure GENCODE v7 TSS expression. If a TSS is shared by transcripts t1,... tn, its expression in an RNA-Seq experiment will be defined as the sum of the RPKM of transcripts […]