Updating RNA-Seq analyses after re-annotation.

ABSTRACT:

Unlabelled

The estimation of isoform abundances from RNA-Seq data requires a time-intensive step of mapping reads to either an assembled or previously annotated transcriptome, followed by an optimization procedure for deconvolution of multi-mapping reads. These procedures are essential for downstream analysis such as differential expression. In cases where it is desirable to adjust the underlying annotation, for example, on the discovery of novel isoforms or errors in existing annotations, current pipelines must be rerun from scratch. This makes it difficult to update abundance estimates after re-annotation, or to explore the effect of changes in the transcriptome on analyses. We present a novel efficient algorithm for updating abundance estimates from RNA-Seq experiments on re-ann

SUBMITTER: Roberts A 

PROVIDER: S-EPMC3694665 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature