Additional file 42.

The pipeline of RNA-seq data analysis in this study. The pipeline involves five steps: read alignment and junction prediction, the filter of false positive junctions, annotation of AS events, global comparison of AS and the identification of differential AS events. To estimate thresholds for filtering false positive junctions, two datasets of random and annotated splice junctions were created. The random splice junctions dataset was created by joining each annotated 5′ donor sequence (90/74 bp from 5′SSs) and the annotated 3′ donor sequence (90/74 bp from 3′SSs) located on a different chromosome. The annotated splice junctions dataset was created by joining each annotated 5′ donor sequence (90/74 bp from 5′SSs) and the annotated 3′ donor sequence (90/74 bp from 3′SSs) in order based on the gene annotation.

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Cui et al. Genome Biology 2014 15:R1   doi:10.1186/gb-2014-15-1-r1