Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data.

ABSTRACT: Transcript quantification is a long-standing problem in genomics and estimating the relative abundance of alternatively-spliced isoforms from the same transcript is an important special case. Both problems have recently been illuminated by high-throughput RNA sequencing experiments which are quickly generating large amounts of data. However, much of the signal present in this data is corrupted or obscured by biases resulting in non-uniform and non-proportional representation of sequences from different transcripts. Many existing analyses attempt to deal with these and other biases with various task-specific approaches, which makes direct comparison between them difficult. However, two popular tools for isoform quantification, MISO and Cufflinks, have adopted a general probabilistic framewo

SUBMITTER: Kakaradov B 

PROVIDER: S-EPMC3330053 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature