Variant Calling Using RNA-seq Data, and Splice Isoform Analysis (11/2/2015)

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.

Disclaimer: This text was selected and edited based on genuine communications that took place between a customer and AccuraScience data analysis team at specified dates and times. The editing was made to protect the customer's privacy and for brevity. The edited text may or may not have been reviewed and approved by the customer. AccuraScience is solely responsible for the accuracy of the information reflected in this text.