SCISSOR: a framework for identifying structural changes in RNA transcripts.

ABSTRACT: High-throughput sequencing protocols such as RNA-seq have made it possible to interrogate the sequence, structure and abundance of RNA transcripts at higher resolution than previous microarray and other molecular techniques. While many computational tools have been proposed for identifying mRNA variation through differential splicing/alternative exon usage, challenges in its analysis remain. Here, we propose a framework for unbiased and robust discovery of aberrant RNA transcript structures using short read sequencing data based on shape changes in an RNA-seq coverage profile. Shape changes in selecting sample outliers in RNA-seq, SCISSOR, is a series of procedures for transforming and normalizing base-level RNA sequencing coverage data in a transcript independent manner, followed by a sta

SUBMITTER: Choi HY 

PROVIDER: S-EPMC7804101 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature