Indel detection from DNA and RNA sequencing data with transIndel.
作者： Rendong Yang , Jamie L. Van Etten , Scott M. Dehm
DOI: 10.1186/S12864-018-4671-4
关键词:
摘要: Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized large indels splicing events RNA-seq data. Here, we developed transIndel, splice-aware algorithm that parses the chimeric alignments predicted by short read aligner reconstructs mid-sized insertions based on linear split reads DNA-seq or TransIndel exhibits competitive superior performance over eight state-of-the-art indel detection tools benchmarks using both synthetic real Additionally, applied transIndel datasets 333 primary prostate cancer patients The Cancer Genome Atlas (TCGA) 59 metastatic AACR-PCF Stand-Up- To-Cancer (SU2C) studies. enhanced taxonomy DNA- RNA-level alterations identifying recurrent FOXA1 as well exitron genes implicated disease progression. Our study demonstrates is robust tool for elucidation medium- large-sized Including discovery efforts leads significant improvements sensitivity identification med-sized missed DNA-seq, reveals non-canonical RNA-splicing pathology.
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