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

ABSTRACT: Different Library Sample Preparation (LSP) allow the detection of a large common set of isoforms. However, each LSP also detects a smaller set of isoforms which are characterized both by lower coverage and lower FPKM than that observed for the common ones among LSPs. This characteristic is particularly critical in case of low input RNA NuGEN v2 LSP. The effect of statistical detection of alternative splicing considering low input LSP (NuGEN v2) with respect to high input LSP (TruSeq) was studied using a benchmark dataset, in which both synthetic reads and reads generated from high and low input LSPs were spiked-in. Statistical detection of alternative splicing was done using prototypes of bioinformatics analysis for isoform-reconstruction and exon-level analysis.

ORGANISM(S): Mus musculus

PROVIDER: GSE58001 | GEO | 2014/05/28

SECONDARY ACCESSION(S): PRJNA248716

REPOSITORIES: GEO

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

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