Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis.

ABSTRACT:

Background

RNA-Seq provides remarkable power in the area of biomarkers discovery and disease characterization. Two crucial steps that affect RNA-Seq experiment results are Library Sample Preparation (LSP) and Bioinformatics Analysis (BA). This work describes an evaluation of the combined effect of LSP methods and BA tools in the detection of splice variants.

Results

Different LSPs (TruSeq unstranded/stranded, ScriptSeq, NuGEN) allowed the detection of a large common set of splice variants. However, each LSP also detected a small set of unique transcripts that are characterized by a low coverage and/or FPKM. This effect was particularly evident using the low input RNA NuGEN v2 protocol. A benchmark dataset, in which synthetic reads as well as reads generated from standard (Il

SUBMITTER: Carrara M 

PROVIDER: S-EPMC4464605 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature