Mon, Nov 2, 2015 at 9:13 AM
Customer: Could you tell me if your group can use raw RNA-seq data to identify indels, splice variants, and isoforms?
Mon, Nov 2, 2015 at 11:22 AM
AccuraScience LB: Variant calling (including SNV and Indel calling) for RNA-seq data isn't much different from variant calling for whole-genome sequencing or exome sequencing data. The GATK pipeline would work fine. However, the nature of RNA-seq data (in particular, the wide difference in depths (or expression levels) across genes) determines that SNV and Indel calling for lowly expressed genes will be less confident.
A few methods are available for determining splice variants using RNA-seq data. Besides the general RNA-seq analysis tool Cufflinks (which does expression quantification better than splice variant analysis), MISO and SpliceTrap are more specialized in analyzing splice variants.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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